rs742208

Positions:

• chr6-15668430-A-G

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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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;