dbSNP rs17115149: PFN1P11:n.*50C>A (chr10-102837961-G-T) – ACMG Classification: Benign (-20 pts)

Variant summary

Our verdict is Benign. The variant received -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The ENST00000445829.1(PFN1P11):n.*50C>A variant causes a downstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00421 in 169,362 control chromosomes in the GnomAD database, including 24 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.0041 ( 19 hom., cov: 32)

Exomes 𝑓: 0.0054 ( 5 hom. )

Consequence

PFN1P11
ENST00000445829.1 downstream_gene

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: 0.353

Publications

11 publications found

Variant links:

Genes affected

PFN1P11 (HGNC:42994): (profilin 1 pseudogene 11)

PFN1P11 links:

Genome browser will be placed here

new If you want to explore the variant's impact on the transcript ENST00000445829.1, check out the Mutation Effect Viewer. This is especially useful for frameshift variants or if you want to visualize the effect of exon loss / intron retention.

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -20 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.95).

BP6

Variant 10-102837961-G-T is Benign according to our data. Variant chr10-102837961-G-T is described in ClinVar as Benign. ClinVar VariationId is 1165814.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.0643 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000445829.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PFN1P11	ENST00000445829.1	TSL:6	n.*50C>A		downstream_gene	N/A

Frequencies

GnomAD3 genomes

AF:

0.00406

AC:

617

AN:

152088

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00101

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.000852

Gnomad ASJ

AF:

0.00202

Gnomad EAS

AF:

0.0701

Gnomad SAS

AF:

0.0218

Gnomad FIN

AF:

0.00340

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.000618

Gnomad OTH

AF:

0.00383

GnomAD4 exome

AF:

0.00536

AC:

AN:

17156

Hom.:

Cov.:

AF XY:

0.00623

AC XY:

AN XY:

8822

show subpopulations

African (AFR)

AF:

0.00

AC:

AN:

128

American (AMR)

AF:

0.00

AC:

AN:

2496

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

130

East Asian (EAS)

AF:

0.0567

AC:

AN:

688

South Asian (SAS)

AF:

0.0144

AC:

AN:

1738

European-Finnish (FIN)

AF:

0.00609

AC:

AN:

3450

Middle Eastern (MID)

AF:

0.00

AC:

AN:

European-Non Finnish (NFE)

AF:

0.000509

AC:

AN:

7866

Other (OTH)

AF:

0.00470

AC:

AN:

638

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.496

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.00408

AC:

621

AN:

152206

Hom.:

Cov.:

AF XY:

0.00503

AC XY:

374

AN XY:

74412

show subpopulations

African (AFR)

AF:

0.00101

AC:

AN:

41536

American (AMR)

AF:

0.000851

AC:

AN:

15284

Ashkenazi Jewish (ASJ)

AF:

0.00202

AC:

AN:

3472

East Asian (EAS)

AF:

0.0703

AC:

364

AN:

5180

South Asian (SAS)

AF:

0.0222

AC:

107

AN:

4818

European-Finnish (FIN)

AF:

0.00340

AC:

AN:

10594

Middle Eastern (MID)

AF:

0.00

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.000618

AC:

AN:

68004

Other (OTH)

AF:

0.00473

AC:

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.498

Heterozygous variant carriers

125

156

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

100

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.00103

Hom.:

Bravo

AF:

0.00357

Asia WGS

AF:

0.0420

AC:

147

AN:

3478

ClinVar

ClinVar submissions

Significance:Benign

Revision:criteria provided, multiple submitters, no conflicts

View on ClinVar

Pathogenic

VUS

Benign

Condition

not provided (2)

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.95

CADD

Benign

(source)

DANN

Benign

0.55

PhyloP100

0.35

PromoterAI

-0.0070

Neutral

(source)

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over