rs742208

Variant names:

• chr6-15668430-A-G
• rs742208

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 0.17 in 152,172 control chromosomes in the GnomAD database, including 3,294 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 (3294 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.61

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.353 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: 0.170 AC: 25915 AN: 152056 Hom.: 3299 Cov.: 32

Gnomad AFR AF: 0.358

Gnomad AMI AF: 0.0757

Gnomad AMR AF: 0.170

Gnomad ASJ AF: 0.0827

Gnomad EAS AF: 0.00231

Gnomad SAS AF: 0.0583

Gnomad FIN AF: 0.0704

Gnomad MID AF: 0.196

Gnomad NFE AF: 0.0989

Gnomad OTH AF: 0.150

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

GnomAD4 genome AF: 0.170 AC: 25925 AN: 152172 Hom.: 3294 Cov.: 32 AF XY: 0.166 AC XY: 12331 AN XY: 74396

Gnomad4 AFR AF: 0.358

Gnomad4 AMR AF: 0.170

Gnomad4 ASJ AF: 0.0827

Gnomad4 EAS AF: 0.00212

Gnomad4 SAS AF: 0.0589

Gnomad4 FIN AF: 0.0704

Gnomad4 NFE AF: 0.0988

Gnomad4 OTH AF: 0.148

Alfa AF: 0.110 Hom.: 1252

Bravo AF: 0.188

Asia WGS AF: 0.0490 AC: 171 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.013
DANN	Benign	0.39

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs742208; hg19: chr6-15668661;