dbSNP rs10514235: ENSG00000265844:n.210-6917G>A (chr18-77198522-G-A) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000584843.1(ENSG00000265844):n.210-6917G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.049 in 152,226 control chromosomes in the GnomAD database, including 324 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.049 ( 324 hom., cov: 33)

Consequence

ENSG00000265844
ENST00000584843.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.0680

Publications

2 publications found

Variant links:

Genes affected

ENSG00000265844 (HGNC:):

ENSG00000265844 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.93).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.133 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000265844	ENST00000584843.1 link	n.210-6917G>A		intron_variant	Intron 2 of 4	4
ENSG00000265844	ENST00000843890.1 link	n.538+9935G>A		intron_variant	Intron 3 of 3

Frequencies

GnomAD3 genomes

AF:

0.0490

AC:

7449

AN:

152108

Hom.:

321

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00961

Gnomad AMI

AF:

0.192

Gnomad AMR

AF:

0.111

Gnomad ASJ

AF:

0.0265

Gnomad EAS

AF:

0.142

Gnomad SAS

AF:

0.0673

Gnomad FIN

AF:

0.0980

Gnomad MID

AF:

0.00949

Gnomad NFE

AF:

0.0426

Gnomad OTH

AF:

0.0407

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome

AF:

0.0490

AC:

7464

AN:

152226

Hom.:

324

Cov.:

AF XY:

0.0525

AC XY:

3904

AN XY:

74412

show subpopulations

African (AFR)

AF:

0.00958

AC:

398

AN:

41536

American (AMR)

AF:

0.112

AC:

1710

AN:

15292

Ashkenazi Jewish (ASJ)

AF:

0.0265

AC:

AN:

3468

East Asian (EAS)

AF:

0.142

AC:

733

AN:

5180

South Asian (SAS)

AF:

0.0682

AC:

329

AN:

4826

European-Finnish (FIN)

AF:

0.0980

AC:

1037

AN:

10584

Middle Eastern (MID)

AF:

0.0102

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0426

AC:

2898

AN:

68024

Other (OTH)

AF:

0.0421

AC:

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.498

Heterozygous variant carriers

362

723

1085

1446

1808

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

172

258

344

430

<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:

0.0301

Hom.:

Bravo

AF:

0.0485

Asia WGS

AF:

0.0820

AC:

284

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.93

CADD

Benign

2.0

(source)

DANN

Benign

0.71

PhyloP100

-0.068

Mutation Taster

=100/0

polymorphism

(source)

Splicing

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

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over