rs1157242

Variant names:

• chr8-37181847-C-T
• rs1157242

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.122 in 152,260 control chromosomes in the GnomAD database, including 1,491 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 0.12 (1491 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.68
• Publications: 4 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.175 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: 0.122 AC: 18609 AN: 152142 Hom.: 1491 Cov.: 32

Gnomad AFR AF: 0.0303

Gnomad AMI AF: 0.145

Gnomad AMR AF: 0.101

Gnomad ASJ AF: 0.164

Gnomad EAS AF: 0.000192

Gnomad SAS AF: 0.0656

Gnomad FIN AF: 0.222

Gnomad MID AF: 0.180

Gnomad NFE AF: 0.178

Gnomad OTH AF: 0.139

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

GnomAD4 genome AF: 0.122 AC: 18598 AN: 152260 Hom.: 1491 Cov.: 32 AF XY: 0.122 AC XY: 9044 AN XY: 74430

African (AFR) AF: 0.0302 AC: 1255 AN: 41554

American (AMR) AF: 0.100 AC: 1537 AN: 15306

Ashkenazi Jewish (ASJ) AF: 0.164 AC: 571 AN: 3472

East Asian (EAS) AF: 0.000193 AC: 1 AN: 5190

South Asian (SAS) AF: 0.0650 AC: 314 AN: 4830

European-Finnish (FIN) AF: 0.222 AC: 2357 AN: 10598

Middle Eastern (MID) AF: 0.177 AC: 52 AN: 294

European-Non Finnish (NFE) AF: 0.178 AC: 12089 AN: 67996

Other (OTH) AF: 0.138 AC: 290 AN: 2108

Alfa AF: 0.134 Hom.: 1276

Bravo AF: 0.110

Asia WGS AF: 0.0250 AC: 87 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	11
DANN	Benign	0.33
PhyloP100		1.7

Splicing

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

Other links and lift over

dbSNP: rs1157242; hg19: chr8-37039365;