chr3-77695543-A-C

Variant names:

• chr3-77695543-A-C
• rs13095558

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 0.486 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

ACMG classification

Verdict is Benign. Variant got -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

Gnomad4 AFR AF: 0.408

Gnomad4 AMR AF: 0.495

Gnomad4 ASJ AF: 0.537

Gnomad4 EAS AF: 0.508

Gnomad4 SAS AF: 0.621

Gnomad4 FIN AF: 0.481

Gnomad4 NFE AF: 0.518

Gnomad4 OTH AF: 0.510

Alfa AF: 0.501 Hom.: 10425

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs13095558; hg19: chr3-77744694;