10-121477406-G-A

Variant names:

• chr10-121477406-G-A
• rs3135831

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.335 in 152,066 control chromosomes in the GnomAD database, including 10,340 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 0.33 (10340 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -4.76
• Publications: 7 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.467 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.335 AC: 50937 AN: 151946 Hom.: 10342 Cov.: 32

Gnomad AFR AF: 0.102

Gnomad AMI AF: 0.356

Gnomad AMR AF: 0.476

Gnomad ASJ AF: 0.499

Gnomad EAS AF: 0.253

Gnomad SAS AF: 0.430

Gnomad FIN AF: 0.305

Gnomad MID AF: 0.386

Gnomad NFE AF: 0.440

Gnomad OTH AF: 0.363

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

GnomAD4 genome AF: 0.335 AC: 50931 AN: 152066 Hom.: 10340 Cov.: 32 AF XY: 0.334 AC XY: 24808 AN XY: 74338

African (AFR) AF: 0.102 AC: 4229 AN: 41506

American (AMR) AF: 0.477 AC: 7282 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.499 AC: 1732 AN: 3470

East Asian (EAS) AF: 0.253 AC: 1304 AN: 5158

South Asian (SAS) AF: 0.429 AC: 2061 AN: 4806

European-Finnish (FIN) AF: 0.305 AC: 3216 AN: 10558

Middle Eastern (MID) AF: 0.395 AC: 116 AN: 294

European-Non Finnish (NFE) AF: 0.440 AC: 29906 AN: 67970

Other (OTH) AF: 0.360 AC: 760 AN: 2110

Alfa AF: 0.420 Hom.: 30794

Bravo AF: 0.340

Asia WGS AF: 0.310 AC: 1077 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.025
DANN	Benign	0.94
PhyloP100		-4.8

Splicing

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

Other links and lift over

dbSNP: rs3135831; hg19: chr10-123236920; COSMIC: COSV61145990;