chr3-77695543-A-C

Variant names:

• chr3-77695543-A-C
• rs13095558

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 0.486 in 152,012 control chromosomes in the GnomAD database, including 18,354 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 0.49 (18354 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.962
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.603 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: 0.487 AC: 73897 AN: 151892 Hom.: 18342 Cov.: 32

Gnomad AFR AF: 0.408

Gnomad AMI AF: 0.516

Gnomad AMR AF: 0.495

Gnomad ASJ AF: 0.537

Gnomad EAS AF: 0.509

Gnomad SAS AF: 0.620

Gnomad FIN AF: 0.481

Gnomad MID AF: 0.563

Gnomad NFE AF: 0.518

Gnomad OTH AF: 0.506

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

GnomAD4 genome AF: 0.486 AC: 73946 AN: 152012 Hom.: 18354 Cov.: 32 AF XY: 0.489 AC XY: 36345 AN XY: 74288

African (AFR) AF: 0.408 AC: 16895 AN: 41434

American (AMR) AF: 0.495 AC: 7555 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.537 AC: 1862 AN: 3470

East Asian (EAS) AF: 0.508 AC: 2626 AN: 5166

South Asian (SAS) AF: 0.621 AC: 2995 AN: 4820

European-Finnish (FIN) AF: 0.481 AC: 5076 AN: 10556

Middle Eastern (MID) AF: 0.554 AC: 163 AN: 294

European-Non Finnish (NFE) AF: 0.518 AC: 35227 AN: 67986

Other (OTH) AF: 0.510 AC: 1077 AN: 2112

Alfa AF: 0.501 Hom.: 11532

Bravo AF: 0.480

Asia WGS AF: 0.585 AC: 2036 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.3
DANN	Benign	0.48
PhyloP100		-0.96

Splicing

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

Other links and lift over

dbSNP: rs13095558; hg19: chr3-77744694;