3-96319512-C-T

Variant names:

• chr3-96319512-C-T
• rs10511154

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 0.627 in 152,068 control chromosomes in the GnomAD database, including 30,677 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 0.63 (30677 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.778
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.05).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.802 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: 0.627 AC: 95257 AN: 151952 Hom.: 30635 Cov.: 33

Gnomad AFR AF: 0.759

Gnomad AMI AF: 0.566

Gnomad AMR AF: 0.579

Gnomad ASJ AF: 0.452

Gnomad EAS AF: 0.822

Gnomad SAS AF: 0.688

Gnomad FIN AF: 0.611

Gnomad MID AF: 0.554

Gnomad NFE AF: 0.551

Gnomad OTH AF: 0.604

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

GnomAD4 genome AF: 0.627 AC: 95354 AN: 152068 Hom.: 30677 Cov.: 33 AF XY: 0.631 AC XY: 46854 AN XY: 74310

African (AFR) AF: 0.759 AC: 31517 AN: 41520

American (AMR) AF: 0.579 AC: 8840 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.452 AC: 1567 AN: 3468

East Asian (EAS) AF: 0.822 AC: 4241 AN: 5158

South Asian (SAS) AF: 0.687 AC: 3313 AN: 4820

European-Finnish (FIN) AF: 0.611 AC: 6464 AN: 10586

Middle Eastern (MID) AF: 0.548 AC: 159 AN: 290

European-Non Finnish (NFE) AF: 0.551 AC: 37467 AN: 67954

Other (OTH) AF: 0.603 AC: 1272 AN: 2108

Alfa AF: 0.607 Hom.: 3578

Bravo AF: 0.632

Asia WGS AF: 0.789 AC: 2744 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	1.2
DANN	Benign	0.18
PhyloP100		-0.78

Splicing

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

Other links and lift over

dbSNP: rs10511154; hg19: chr3-96038356;