rs667538

Variant names:

• chr6-160317888-T-G
• rs667538

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 2 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

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

African (AFR) AF: 0.587 AC: 24362 AN: 41468

American (AMR) AF: 0.524 AC: 8006 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.609 AC: 2113 AN: 3472

East Asian (EAS) AF: 0.422 AC: 2181 AN: 5172

South Asian (SAS) AF: 0.479 AC: 2310 AN: 4826

European-Finnish (FIN) AF: 0.640 AC: 6750 AN: 10552

Middle Eastern (MID) AF: 0.612 AC: 180 AN: 294

European-Non Finnish (NFE) AF: 0.678 AC: 46063 AN: 67968

Other (OTH) AF: 0.618 AC: 1306 AN: 2112

Alfa AF: 0.629 Hom.: 5277

Bravo AF: 0.610

Asia WGS AF: 0.450 AC: 1568 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	3.2
DANN	Benign	0.45
PhyloP100		-0.063

Splicing

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

Other links and lift over

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