6-160335005-C-T

Variant names:

• chr6-160335005-C-T
• rs316170

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 0.639 in 151,860 control chromosomes in the GnomAD database, including 31,274 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 (31274 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.434
• Publications: 6 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.668 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.639 AC: 96939 AN: 151742 Hom.: 31237 Cov.: 31

Gnomad AFR AF: 0.672

Gnomad AMI AF: 0.546

Gnomad AMR AF: 0.530

Gnomad ASJ AF: 0.606

Gnomad EAS AF: 0.449

Gnomad SAS AF: 0.462

Gnomad FIN AF: 0.639

Gnomad MID AF: 0.639

Gnomad NFE AF: 0.673

Gnomad OTH AF: 0.632

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

GnomAD4 genome AF: 0.639 AC: 97020 AN: 151860 Hom.: 31274 Cov.: 31 AF XY: 0.633 AC XY: 46944 AN XY: 74194

African (AFR) AF: 0.672 AC: 27842 AN: 41424

American (AMR) AF: 0.529 AC: 8070 AN: 15252

Ashkenazi Jewish (ASJ) AF: 0.606 AC: 2102 AN: 3468

East Asian (EAS) AF: 0.449 AC: 2306 AN: 5134

South Asian (SAS) AF: 0.464 AC: 2228 AN: 4806

European-Finnish (FIN) AF: 0.639 AC: 6713 AN: 10510

Middle Eastern (MID) AF: 0.633 AC: 186 AN: 294

European-Non Finnish (NFE) AF: 0.673 AC: 45751 AN: 67954

Other (OTH) AF: 0.628 AC: 1328 AN: 2114

Alfa AF: 0.661 Hom.: 51332

Bravo AF: 0.634

Asia WGS AF: 0.452 AC: 1574 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.47
DANN	Benign	0.28
PhyloP100		-0.43

Splicing

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

Other links and lift over

dbSNP: rs316170; hg19: chr6-160756037;