6-15664533-G-C

Variant names:

• chr6-15664533-G-C
• rs2743852

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 0.175 in 118,904 control chromosomes in the GnomAD database, including 2,040 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 0.17 (2040 hom., cov: 24)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0120
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.32 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: 0.175 AC: 20799 AN: 118832 Hom.: 2044 Cov.: 24

Gnomad AFR AF: 0.326

Gnomad AMI AF: 0.0939

Gnomad AMR AF: 0.213

Gnomad ASJ AF: 0.0825

Gnomad EAS AF: 0.00295

Gnomad SAS AF: 0.0589

Gnomad FIN AF: 0.125

Gnomad MID AF: 0.248

Gnomad NFE AF: 0.111

Gnomad OTH AF: 0.160

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

GnomAD4 genome AF: 0.175 AC: 20803 AN: 118904 Hom.: 2040 Cov.: 24 AF XY: 0.177 AC XY: 9845 AN XY: 55616

African (AFR) AF: 0.326 AC: 10728 AN: 32952

American (AMR) AF: 0.213 AC: 2255 AN: 10606

Ashkenazi Jewish (ASJ) AF: 0.0825 AC: 251 AN: 3044

East Asian (EAS) AF: 0.00268 AC: 10 AN: 3728

South Asian (SAS) AF: 0.0599 AC: 225 AN: 3756

European-Finnish (FIN) AF: 0.125 AC: 641 AN: 5142

Middle Eastern (MID) AF: 0.247 AC: 49 AN: 198

European-Non Finnish (NFE) AF: 0.111 AC: 6327 AN: 57178

Other (OTH) AF: 0.158 AC: 249 AN: 1576

Alfa AF: 0.104 Hom.: 160

Bravo AF: 0.158

Asia WGS AF: 0.0350 AC: 123 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	4.3
DANN	Benign	0.58
PhyloP100		-0.012

Splicing

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

Other links and lift over

dbSNP: rs2743852; hg19: chr6-15664764;