3-80319313-T-C

Variant names:

• chr3-80319313-T-C
• rs10511112

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 0.0588 in 152,128 control chromosomes in the GnomAD database, including 277 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 0.059 (277 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.498
• Publications: 9 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0716 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: 0.0588 AC: 8937 AN: 152010 Hom.: 278 Cov.: 32

Gnomad AFR AF: 0.0396

Gnomad AMI AF: 0.0581

Gnomad AMR AF: 0.0652

Gnomad ASJ AF: 0.0447

Gnomad EAS AF: 0.0728

Gnomad SAS AF: 0.0514

Gnomad FIN AF: 0.0312

Gnomad MID AF: 0.0791

Gnomad NFE AF: 0.0733

Gnomad OTH AF: 0.0627

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

GnomAD4 genome AF: 0.0588 AC: 8940 AN: 152128 Hom.: 277 Cov.: 32 AF XY: 0.0571 AC XY: 4243 AN XY: 74366

African (AFR) AF: 0.0396 AC: 1643 AN: 41494

American (AMR) AF: 0.0651 AC: 996 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.0447 AC: 155 AN: 3468

East Asian (EAS) AF: 0.0728 AC: 376 AN: 5164

South Asian (SAS) AF: 0.0513 AC: 247 AN: 4818

European-Finnish (FIN) AF: 0.0312 AC: 330 AN: 10592

Middle Eastern (MID) AF: 0.0850 AC: 25 AN: 294

European-Non Finnish (NFE) AF: 0.0733 AC: 4984 AN: 67986

Other (OTH) AF: 0.0621 AC: 131 AN: 2110

Alfa AF: 0.0657 Hom.: 46

Bravo AF: 0.0610

Asia WGS AF: 0.0840 AC: 296 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	2.0
DANN	Benign	0.77
PhyloP100		-0.50

Splicing

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

Other links and lift over

dbSNP: rs10511112; hg19: chr3-80368463;