dbSNP rs10485999: ENSG00000305877:n.115-4497C>T (chr7-97514674-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 ENST00000813676.1(ENSG00000305877):n.115-4497C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0274 in 152,188 control chromosomes in the GnomAD database, including 88 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 0.027 ( 88 hom., cov: 32)

Consequence

ENSG00000305877
ENST00000813676.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.577

Publications

1 publications found

Variant links:

Genes affected

ENSG00000305877 (HGNC:58698):

ENSG00000305877 links:

LOC105375416 (HGNC:):

LOC105375416 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=-0.91).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.107 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105375416	XR_001745293.1 link	n.22-4497C>T		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000305877	ENST00000813676.1 link	n.115-4497C>T		intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes

AF:

0.0273

AC:

4146

AN:

152070

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0262

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.0193

Gnomad ASJ

AF:

0.0150

Gnomad EAS

AF:

0.114

Gnomad SAS

AF:

0.0483

Gnomad FIN

AF:

0.0416

Gnomad MID

AF:

0.0158

Gnomad NFE

AF:

0.0205

Gnomad OTH

AF:

0.0220

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

GnomAD4 genome

AF:

0.0274

AC:

4168

AN:

152188

Hom.:

Cov.:

AF XY:

0.0297

AC XY:

2208

AN XY:

74400

show subpopulations

African (AFR)

AF:

0.0264

AC:

1098

AN:

41532

American (AMR)

AF:

0.0193

AC:

295

AN:

15274

Ashkenazi Jewish (ASJ)

AF:

0.0150

AC:

AN:

3470

East Asian (EAS)

AF:

0.115

AC:

593

AN:

5172

South Asian (SAS)

AF:

0.0484

AC:

233

AN:

4818

European-Finnish (FIN)

AF:

0.0416

AC:

441

AN:

10594

Middle Eastern (MID)

AF:

0.0170

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0205

AC:

1394

AN:

68010

Other (OTH)

AF:

0.0270

AC:

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

201

401

602

802

1003

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

104

156

208

260

<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:

0.0118

Hom.:

Bravo

AF:

0.0268

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.91

CADD

Benign

0.18

(source)

DANN

Benign

0.56

PhyloP100

-0.58

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