rs747158

Variant names:

• chr6-37756637-C-T
• rs747158

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 0.0995 in 152,266 control chromosomes in the GnomAD database, including 1,071 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 0.10 (1071 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.501

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.75).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.145 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: 0.0996 AC: 15151 AN: 152148 Hom.: 1071 Cov.: 32

Gnomad AFR AF: 0.0259

Gnomad AMI AF: 0.135

Gnomad AMR AF: 0.0955

Gnomad ASJ AF: 0.253

Gnomad EAS AF: 0.00327

Gnomad SAS AF: 0.0357

Gnomad FIN AF: 0.100

Gnomad MID AF: 0.168

Gnomad NFE AF: 0.148

Gnomad OTH AF: 0.127

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

GnomAD4 genome AF: 0.0995 AC: 15151 AN: 152266 Hom.: 1071 Cov.: 32 AF XY: 0.0950 AC XY: 7071 AN XY: 74446

Gnomad4 AFR AF: 0.0258

Gnomad4 AMR AF: 0.0953

Gnomad4 ASJ AF: 0.253

Gnomad4 EAS AF: 0.00328

Gnomad4 SAS AF: 0.0353

Gnomad4 FIN AF: 0.100

Gnomad4 NFE AF: 0.148

Gnomad4 OTH AF: 0.126

Alfa AF: 0.130 Hom.: 744

Bravo AF: 0.0999

Asia WGS AF: 0.0230 AC: 80 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.75
CADD	Benign	11
DANN	Benign	0.78

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs747158; hg19: chr6-37724413;