rs667538

chr6-160317888-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 0.617 in 152,054 control chromosomes in the GnomAD database, including 29,213 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 0.62 (29213 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0630

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• 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: 0.617 AC: 93701 AN: 151934 Hom.: 29189 Cov.: 32

Gnomad AFR AF: 0.587

Gnomad AMI AF: 0.547

Gnomad AMR AF: 0.525

Gnomad ASJ AF: 0.609

Gnomad EAS AF: 0.422

Gnomad SAS AF: 0.477

Gnomad FIN AF: 0.640

Gnomad MID AF: 0.620

Gnomad NFE AF: 0.678

Gnomad OTH AF: 0.622

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

GnomAD4 genome AF: 0.617 AC: 93770 AN: 152054 Hom.: 29213 Cov.: 32 AF XY: 0.611 AC XY: 45411 AN XY: 74330

Gnomad4 AFR AF: 0.587

Gnomad4 AMR AF: 0.524

Gnomad4 ASJ AF: 0.609

Gnomad4 EAS AF: 0.422

Gnomad4 SAS AF: 0.479

Gnomad4 FIN AF: 0.640

Gnomad4 NFE AF: 0.678

Gnomad4 OTH AF: 0.618

Alfa AF: 0.630 Hom.: 5135

Bravo AF: 0.610

Asia WGS AF: 0.450 AC: 1568 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	3.2
Dann	Benign	0.45

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs667538; hg19: chr6-160738920; COSMIC: COSV70616842;