rs2743852

Positions:

• chr6-15664533-G-C
• chr6-15664533-G-T

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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

Gnomad4 AFR AF: 0.326

Gnomad4 AMR AF: 0.213

Gnomad4 ASJ AF: 0.0825

Gnomad4 EAS AF: 0.00268

Gnomad4 SAS AF: 0.0599

Gnomad4 FIN AF: 0.125

Gnomad4 NFE AF: 0.111

Gnomad4 OTH AF: 0.158

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2743852; hg19: chr6-15664764;