rs6762218

Variant names:

• chr3-135863451-C-T
• rs6762218

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 0.235 in 151,870 control chromosomes in the GnomAD database, including 4,680 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 (4680 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.290
• Publications: 2 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 = 0.333 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: 0.235 AC: 35703 AN: 151752 Hom.: 4664 Cov.: 31

Gnomad AFR AF: 0.337

Gnomad AMI AF: 0.237

Gnomad AMR AF: 0.153

Gnomad ASJ AF: 0.180

Gnomad EAS AF: 0.00367

Gnomad SAS AF: 0.155

Gnomad FIN AF: 0.278

Gnomad MID AF: 0.171

Gnomad NFE AF: 0.212

Gnomad OTH AF: 0.223

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

GnomAD4 genome AF: 0.235 AC: 35755 AN: 151870 Hom.: 4680 Cov.: 31 AF XY: 0.235 AC XY: 17422 AN XY: 74180

African (AFR) AF: 0.337 AC: 13967 AN: 41404

American (AMR) AF: 0.153 AC: 2332 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.180 AC: 626 AN: 3470

East Asian (EAS) AF: 0.00368 AC: 19 AN: 5160

South Asian (SAS) AF: 0.156 AC: 749 AN: 4798

European-Finnish (FIN) AF: 0.278 AC: 2921 AN: 10500

Middle Eastern (MID) AF: 0.173 AC: 51 AN: 294

European-Non Finnish (NFE) AF: 0.212 AC: 14409 AN: 67964

Other (OTH) AF: 0.221 AC: 466 AN: 2112

Alfa AF: 0.212 Hom.: 5906

Bravo AF: 0.230

Asia WGS AF: 0.0860 AC: 301 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	1.2
DANN	Benign	0.48
PhyloP100		-0.29

Splicing

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

Other links and lift over

dbSNP: rs6762218; hg19: chr3-135582293;