6-160346151-C-T

Variant names:

• chr6-160346151-C-T
• rs569919

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 0.236 in 151,898 control chromosomes in the GnomAD database, including 4,568 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 0.24 (4568 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.549
• Publications: 10 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.283 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: 0.236 AC: 35820 AN: 151784 Hom.: 4569 Cov.: 32

Gnomad AFR AF: 0.140

Gnomad AMI AF: 0.181

Gnomad AMR AF: 0.182

Gnomad ASJ AF: 0.328

Gnomad EAS AF: 0.295

Gnomad SAS AF: 0.283

Gnomad FIN AF: 0.288

Gnomad MID AF: 0.272

Gnomad NFE AF: 0.286

Gnomad OTH AF: 0.257

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

GnomAD4 genome AF: 0.236 AC: 35840 AN: 151898 Hom.: 4568 Cov.: 32 AF XY: 0.237 AC XY: 17618 AN XY: 74222

African (AFR) AF: 0.141 AC: 5826 AN: 41438

American (AMR) AF: 0.182 AC: 2783 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.328 AC: 1140 AN: 3472

East Asian (EAS) AF: 0.295 AC: 1517 AN: 5140

South Asian (SAS) AF: 0.284 AC: 1362 AN: 4800

European-Finnish (FIN) AF: 0.288 AC: 3030 AN: 10536

Middle Eastern (MID) AF: 0.265 AC: 78 AN: 294

European-Non Finnish (NFE) AF: 0.286 AC: 19402 AN: 67930

Other (OTH) AF: 0.255 AC: 537 AN: 2104

Alfa AF: 0.273 Hom.: 11463

Bravo AF: 0.226

Asia WGS AF: 0.294 AC: 1020 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	5.2
DANN	Benign	0.23
PhyloP100		0.55

Splicing

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

Other links and lift over

dbSNP: rs569919; hg19: chr6-160767183;