rs316169

Positions:

• chr6-160334625-T-G

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 0.636 in 152,028 control chromosomes in the GnomAD database, including 31,049 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 0.64 (31049 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.647

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.673 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: 0.636 AC: 96662 AN: 151910 Hom.: 31019 Cov.: 31

Gnomad AFR AF: 0.652

Gnomad AMI AF: 0.550

Gnomad AMR AF: 0.532

Gnomad ASJ AF: 0.608

Gnomad EAS AF: 0.450

Gnomad SAS AF: 0.479

Gnomad FIN AF: 0.639

Gnomad MID AF: 0.630

Gnomad NFE AF: 0.678

Gnomad OTH AF: 0.634

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

GnomAD4 genome AF: 0.636 AC: 96736 AN: 152028 Hom.: 31049 Cov.: 31 AF XY: 0.630 AC XY: 46827 AN XY: 74298

Gnomad4 AFR AF: 0.652

Gnomad4 AMR AF: 0.531

Gnomad4 ASJ AF: 0.608

Gnomad4 EAS AF: 0.450

Gnomad4 SAS AF: 0.481

Gnomad4 FIN AF: 0.639

Gnomad4 NFE AF: 0.678

Gnomad4 OTH AF: 0.629

Alfa AF: 0.642 Hom.: 5337

Bravo AF: 0.632

Asia WGS AF: 0.457 AC: 1592 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.46
DANN	Benign	0.51

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs316169; hg19: chr6-160755657;