6-153950664-G-A

Variant names:

• chr6-153950664-G-A
• rs612665

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 0.799 in 152,102 control chromosomes in the GnomAD database, including 48,930 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 0.80 (48930 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.327
• Publications: 3 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.88 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.799 AC: 121482 AN: 151984 Hom.: 48904 Cov.: 32

Gnomad AFR AF: 0.888

Gnomad AMI AF: 0.838

Gnomad AMR AF: 0.833

Gnomad ASJ AF: 0.671

Gnomad EAS AF: 0.757

Gnomad SAS AF: 0.790

Gnomad FIN AF: 0.823

Gnomad MID AF: 0.671

Gnomad NFE AF: 0.745

Gnomad OTH AF: 0.786

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

GnomAD4 genome AF: 0.799 AC: 121556 AN: 152102 Hom.: 48930 Cov.: 32 AF XY: 0.802 AC XY: 59633 AN XY: 74366

African (AFR) AF: 0.888 AC: 36852 AN: 41502

American (AMR) AF: 0.833 AC: 12724 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.671 AC: 2328 AN: 3468

East Asian (EAS) AF: 0.756 AC: 3910 AN: 5172

South Asian (SAS) AF: 0.788 AC: 3804 AN: 4828

European-Finnish (FIN) AF: 0.823 AC: 8705 AN: 10578

Middle Eastern (MID) AF: 0.670 AC: 197 AN: 294

European-Non Finnish (NFE) AF: 0.745 AC: 50630 AN: 67964

Other (OTH) AF: 0.780 AC: 1643 AN: 2106

Alfa AF: 0.766 Hom.: 5489

Bravo AF: 0.804

Asia WGS AF: 0.756 AC: 2630 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	3.7
DANN	Benign	0.16
PhyloP100		0.33

Splicing

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

Other links and lift over

dbSNP: rs612665; hg19: chr6-154271799;