rs928722

Positions:

• chr6-137652695-C-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 0.159 in 152,108 control chromosomes in the GnomAD database, including 2,132 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 0.16 (2132 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.305

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.206 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: 0.159 AC: 24190 AN: 151990 Hom.: 2131 Cov.: 31

Gnomad AFR AF: 0.110

Gnomad AMI AF: 0.157

Gnomad AMR AF: 0.124

Gnomad ASJ AF: 0.150

Gnomad EAS AF: 0.00193

Gnomad SAS AF: 0.121

Gnomad FIN AF: 0.178

Gnomad MID AF: 0.139

Gnomad NFE AF: 0.209

Gnomad OTH AF: 0.161

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

GnomAD4 genome AF: 0.159 AC: 24195 AN: 152108 Hom.: 2132 Cov.: 31 AF XY: 0.155 AC XY: 11503 AN XY: 74366

Gnomad4 AFR AF: 0.110

Gnomad4 AMR AF: 0.124

Gnomad4 ASJ AF: 0.150

Gnomad4 EAS AF: 0.00193

Gnomad4 SAS AF: 0.121

Gnomad4 FIN AF: 0.178

Gnomad4 NFE AF: 0.209

Gnomad4 OTH AF: 0.160

Alfa AF: 0.181 Hom.: 336

Bravo AF: 0.153

Asia WGS AF: 0.0610 AC: 213 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	7.2
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: rs928722; hg19: chr6-137973832;