rs3135831

Variant names:

• chr10-121477406-G-A
• rs3135831

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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.

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

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

Gnomad4 AFR AF: 0.102

Gnomad4 AMR AF: 0.477

Gnomad4 ASJ AF: 0.499

Gnomad4 EAS AF: 0.253

Gnomad4 SAS AF: 0.429

Gnomad4 FIN AF: 0.305

Gnomad4 NFE AF: 0.440

Gnomad4 OTH AF: 0.360

Alfa AF: 0.428 Hom.: 21499

Bravo AF: 0.340

Asia WGS AF: 0.310 AC: 1077 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

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