chr6-151636579-C-T

Variant names:

• chr6-151636579-C-T
• rs12173570

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 0.203 in 152,064 control chromosomes in the GnomAD database, including 5,177 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 0.20 (5177 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.599
• Publications: 22 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 (AFR) allele frequency at 95% confidence interval = 0.453 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: 0.203 AC: 30833 AN: 151946 Hom.: 5163 Cov.: 32

Gnomad AFR AF: 0.458

Gnomad AMI AF: 0.0713

Gnomad AMR AF: 0.125

Gnomad ASJ AF: 0.109

Gnomad EAS AF: 0.322

Gnomad SAS AF: 0.0919

Gnomad FIN AF: 0.0445

Gnomad MID AF: 0.162

Gnomad NFE AF: 0.0959

Gnomad OTH AF: 0.199

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

GnomAD4 genome AF: 0.203 AC: 30876 AN: 152064 Hom.: 5177 Cov.: 32 AF XY: 0.197 AC XY: 14675 AN XY: 74324

African (AFR) AF: 0.458 AC: 18975 AN: 41414

American (AMR) AF: 0.125 AC: 1905 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.109 AC: 378 AN: 3472

East Asian (EAS) AF: 0.321 AC: 1653 AN: 5142

South Asian (SAS) AF: 0.0919 AC: 443 AN: 4818

European-Finnish (FIN) AF: 0.0445 AC: 472 AN: 10596

Middle Eastern (MID) AF: 0.158 AC: 46 AN: 292

European-Non Finnish (NFE) AF: 0.0958 AC: 6519 AN: 68014

Other (OTH) AF: 0.199 AC: 420 AN: 2112

Alfa AF: 0.133 Hom.: 6104

Bravo AF: 0.223

Asia WGS AF: 0.212 AC: 737 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	1.0
DANN	Benign	0.66
PhyloP100		-0.60

Splicing

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

Other links and lift over

dbSNP: rs12173570; hg19: chr6-151957714;