rs76546355

chr6-31381371-G-A

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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;