6-160333170-T-C

Variant names:

• chr6-160333170-T-C
• rs172722

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 0.597 in 151,886 control chromosomes in the GnomAD database, including 27,501 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 (27501 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -4.78
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.671 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: 0.597 AC: 90676 AN: 151766 Hom.: 27480 Cov.: 32

Gnomad AFR AF: 0.519

Gnomad AMI AF: 0.547

Gnomad AMR AF: 0.516

Gnomad ASJ AF: 0.605

Gnomad EAS AF: 0.449

Gnomad SAS AF: 0.480

Gnomad FIN AF: 0.640

Gnomad MID AF: 0.547

Gnomad NFE AF: 0.677

Gnomad OTH AF: 0.604

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

GnomAD4 genome AF: 0.597 AC: 90742 AN: 151886 Hom.: 27501 Cov.: 32 AF XY: 0.592 AC XY: 43946 AN XY: 74228

African (AFR) AF: 0.520 AC: 21506 AN: 41390

American (AMR) AF: 0.515 AC: 7854 AN: 15254

Ashkenazi Jewish (ASJ) AF: 0.605 AC: 2095 AN: 3460

East Asian (EAS) AF: 0.449 AC: 2311 AN: 5142

South Asian (SAS) AF: 0.482 AC: 2321 AN: 4814

European-Finnish (FIN) AF: 0.640 AC: 6752 AN: 10556

Middle Eastern (MID) AF: 0.541 AC: 159 AN: 294

European-Non Finnish (NFE) AF: 0.677 AC: 45984 AN: 67958

Other (OTH) AF: 0.599 AC: 1262 AN: 2108

Alfa AF: 0.623 Hom.: 3712

Bravo AF: 0.587

Asia WGS AF: 0.448 AC: 1561 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	0.15
DANN	Benign	0.32
PhyloP100		-4.8

Splicing

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

Other links and lift over

dbSNP: rs172722; hg19: chr6-160754202;