6-16175064-A-G

Variant names:

• chr6-16175064-A-G
• rs2038037

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 0.595 in 151,946 control chromosomes in the GnomAD database, including 29,775 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 0.60 (29775 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.682
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.906 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: 0.595 AC: 90325 AN: 151828 Hom.: 29714 Cov.: 30

Gnomad AFR AF: 0.858

Gnomad AMI AF: 0.425

Gnomad AMR AF: 0.624

Gnomad ASJ AF: 0.485

Gnomad EAS AF: 0.929

Gnomad SAS AF: 0.602

Gnomad FIN AF: 0.373

Gnomad MID AF: 0.418

Gnomad NFE AF: 0.447

Gnomad OTH AF: 0.544

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

GnomAD4 genome AF: 0.595 AC: 90446 AN: 151946 Hom.: 29775 Cov.: 30 AF XY: 0.593 AC XY: 44053 AN XY: 74298

African (AFR) AF: 0.858 AC: 35564 AN: 41454

American (AMR) AF: 0.624 AC: 9530 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.485 AC: 1682 AN: 3468

East Asian (EAS) AF: 0.928 AC: 4787 AN: 5156

South Asian (SAS) AF: 0.601 AC: 2891 AN: 4808

European-Finnish (FIN) AF: 0.373 AC: 3947 AN: 10578

Middle Eastern (MID) AF: 0.422 AC: 124 AN: 294

European-Non Finnish (NFE) AF: 0.447 AC: 30374 AN: 67898

Other (OTH) AF: 0.550 AC: 1160 AN: 2110

Alfa AF: 0.494 Hom.: 32628

Bravo AF: 0.627

Asia WGS AF: 0.796 AC: 2768 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.59
DANN	Benign	0.27
PhyloP100		-0.68

Splicing

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

Other links and lift over

dbSNP: rs2038037; hg19: chr6-16175295;