chr6-160313432-T-C

Variant names:

• chr6-160313432-T-C
• rs386618

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 0.462 in 151,786 control chromosomes in the GnomAD database, including 16,676 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 0.46 (16676 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.936
• Publications: 6 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.529 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: 0.462 AC: 70103 AN: 151666 Hom.: 16663 Cov.: 32

Gnomad AFR AF: 0.362

Gnomad AMI AF: 0.431

Gnomad AMR AF: 0.431

Gnomad ASJ AF: 0.555

Gnomad EAS AF: 0.268

Gnomad SAS AF: 0.408

Gnomad FIN AF: 0.527

Gnomad MID AF: 0.532

Gnomad NFE AF: 0.533

Gnomad OTH AF: 0.489

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

GnomAD4 genome AF: 0.462 AC: 70165 AN: 151786 Hom.: 16676 Cov.: 32 AF XY: 0.462 AC XY: 34291 AN XY: 74182

African (AFR) AF: 0.363 AC: 15011 AN: 41406

American (AMR) AF: 0.430 AC: 6569 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.555 AC: 1922 AN: 3464

East Asian (EAS) AF: 0.268 AC: 1388 AN: 5176

South Asian (SAS) AF: 0.411 AC: 1983 AN: 4824

European-Finnish (FIN) AF: 0.527 AC: 5531 AN: 10494

Middle Eastern (MID) AF: 0.521 AC: 150 AN: 288

European-Non Finnish (NFE) AF: 0.533 AC: 36195 AN: 67852

Other (OTH) AF: 0.486 AC: 1026 AN: 2112

Alfa AF: 0.509 Hom.: 4720

Bravo AF: 0.457

Asia WGS AF: 0.351 AC: 1220 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	1.3
DANN	Benign	0.66
PhyloP100		-0.94

Splicing

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

Other links and lift over

dbSNP: rs386618; hg19: chr6-160734464;