rs76546355

Variant names:

• chr6-31381371-G-A
• rs76546355

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 0.0504 in 152,194 control chromosomes in the GnomAD database, including 288 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 0.050 (288 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.17

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.76).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.116 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: 0.0504 AC: 7668 AN: 152076 Hom.: 287 Cov.: 33

Gnomad AFR AF: 0.0111

Gnomad AMI AF: 0.0373

Gnomad AMR AF: 0.0682

Gnomad ASJ AF: 0.0472

Gnomad EAS AF: 0.0594

Gnomad SAS AF: 0.124

Gnomad FIN AF: 0.0649

Gnomad MID AF: 0.0949

Gnomad NFE AF: 0.0617

Gnomad OTH AF: 0.0703

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

GnomAD4 genome AF: 0.0504 AC: 7669 AN: 152194 Hom.: 288 Cov.: 33 AF XY: 0.0522 AC XY: 3881 AN XY: 74414

Gnomad4 AFR AF: 0.0111

Gnomad4 AMR AF: 0.0680

Gnomad4 ASJ AF: 0.0472

Gnomad4 EAS AF: 0.0598

Gnomad4 SAS AF: 0.125

Gnomad4 FIN AF: 0.0649

Gnomad4 NFE AF: 0.0618

Gnomad4 OTH AF: 0.0696

Alfa AF: 0.0518 Hom.: 38

Bravo AF: 0.0491

Asia WGS AF: 0.0780 AC: 272 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.76
CADD	Benign	11
DANN	Benign	0.62

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs76546355; hg19: chr6-31349148;