6-105636010-T-C

Variant names:

• chr6-105636010-T-C
• rs2213753

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 0.363 in 152,032 control chromosomes in the GnomAD database, including 11,659 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 0.36 (11659 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.668
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.582 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: 0.363 AC: 55091 AN: 151912 Hom.: 11626 Cov.: 32

Gnomad AFR AF: 0.587

Gnomad AMI AF: 0.138

Gnomad AMR AF: 0.295

Gnomad ASJ AF: 0.447

Gnomad EAS AF: 0.430

Gnomad SAS AF: 0.357

Gnomad FIN AF: 0.240

Gnomad MID AF: 0.398

Gnomad NFE AF: 0.254

Gnomad OTH AF: 0.360

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

GnomAD4 genome AF: 0.363 AC: 55179 AN: 152032 Hom.: 11659 Cov.: 32 AF XY: 0.363 AC XY: 26996 AN XY: 74310

African (AFR) AF: 0.588 AC: 24361 AN: 41452

American (AMR) AF: 0.295 AC: 4503 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.447 AC: 1550 AN: 3466

East Asian (EAS) AF: 0.429 AC: 2221 AN: 5172

South Asian (SAS) AF: 0.357 AC: 1716 AN: 4808

European-Finnish (FIN) AF: 0.240 AC: 2535 AN: 10584

Middle Eastern (MID) AF: 0.395 AC: 116 AN: 294

European-Non Finnish (NFE) AF: 0.254 AC: 17290 AN: 67974

Other (OTH) AF: 0.361 AC: 761 AN: 2108

Alfa AF: 0.314 Hom.: 1461

Bravo AF: 0.376

Asia WGS AF: 0.413 AC: 1438 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	6.7
DANN	Benign	0.73
PhyloP100		-0.67

Splicing

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

Other links and lift over

dbSNP: rs2213753; hg19: chr6-106083885; COSMIC: COSV70740528;