rs636864

Variant names:

• chr6-149204470-C-T
• rs636864

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 0.282 in 152,072 control chromosomes in the GnomAD database, including 6,963 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 0.28 (6963 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0280
• Publications: 9 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.445 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: 0.282 AC: 42876 AN: 151954 Hom.: 6952 Cov.: 32

Gnomad AFR AF: 0.451

Gnomad AMI AF: 0.237

Gnomad AMR AF: 0.185

Gnomad ASJ AF: 0.205

Gnomad EAS AF: 0.113

Gnomad SAS AF: 0.220

Gnomad FIN AF: 0.226

Gnomad MID AF: 0.272

Gnomad NFE AF: 0.233

Gnomad OTH AF: 0.253

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

GnomAD4 genome AF: 0.282 AC: 42920 AN: 152072 Hom.: 6963 Cov.: 32 AF XY: 0.279 AC XY: 20734 AN XY: 74332

African (AFR) AF: 0.451 AC: 18684 AN: 41464

American (AMR) AF: 0.185 AC: 2824 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.205 AC: 711 AN: 3464

East Asian (EAS) AF: 0.113 AC: 586 AN: 5182

South Asian (SAS) AF: 0.219 AC: 1056 AN: 4828

European-Finnish (FIN) AF: 0.226 AC: 2382 AN: 10540

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

European-Non Finnish (NFE) AF: 0.233 AC: 15843 AN: 67994

Other (OTH) AF: 0.255 AC: 540 AN: 2114

Alfa AF: 0.247 Hom.: 14972

Bravo AF: 0.285

Asia WGS AF: 0.220 AC: 767 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.3
DANN	Benign	0.69
PhyloP100		-0.028

Splicing

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

Other links and lift over

dbSNP: rs636864; hg19: chr6-149525606;