chr6-160334625-T-G

Variant names:

• chr6-160334625-T-G
• rs316169

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 0.636 in 152,028 control chromosomes in the GnomAD database, including 31,049 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 0.64 (31049 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.647
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• 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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.636 AC: 96662 AN: 151910 Hom.: 31019 Cov.: 31

Gnomad AFR AF: 0.652

Gnomad AMI AF: 0.550

Gnomad AMR AF: 0.532

Gnomad ASJ AF: 0.608

Gnomad EAS AF: 0.450

Gnomad SAS AF: 0.479

Gnomad FIN AF: 0.639

Gnomad MID AF: 0.630

Gnomad NFE AF: 0.678

Gnomad OTH AF: 0.634

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

GnomAD4 genome AF: 0.636 AC: 96736 AN: 152028 Hom.: 31049 Cov.: 31 AF XY: 0.630 AC XY: 46827 AN XY: 74298

African (AFR) AF: 0.652 AC: 27050 AN: 41470

American (AMR) AF: 0.531 AC: 8105 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.608 AC: 2110 AN: 3470

East Asian (EAS) AF: 0.450 AC: 2316 AN: 5150

South Asian (SAS) AF: 0.481 AC: 2310 AN: 4806

European-Finnish (FIN) AF: 0.639 AC: 6760 AN: 10578

Middle Eastern (MID) AF: 0.626 AC: 184 AN: 294

European-Non Finnish (NFE) AF: 0.678 AC: 46070 AN: 67960

Other (OTH) AF: 0.629 AC: 1332 AN: 2116

Alfa AF: 0.641 Hom.: 5498

Bravo AF: 0.632

Asia WGS AF: 0.457 AC: 1592 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.46
DANN	Benign	0.51
PhyloP100		-0.65

Splicing

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

Other links and lift over

dbSNP: rs316169; hg19: chr6-160755657;