rs7537266

Variant names:

• chr1-238227855-C-T
• rs7537266

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 0.247 in 151,942 control chromosomes in the GnomAD database, including 4,974 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 0.25 (4974 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.106
• Publications: 7 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.407 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.247 AC: 37564 AN: 151824 Hom.: 4972 Cov.: 32

Gnomad AFR AF: 0.249

Gnomad AMI AF: 0.305

Gnomad AMR AF: 0.180

Gnomad ASJ AF: 0.148

Gnomad EAS AF: 0.331

Gnomad SAS AF: 0.424

Gnomad FIN AF: 0.224

Gnomad MID AF: 0.212

Gnomad NFE AF: 0.251

Gnomad OTH AF: 0.244

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

GnomAD4 genome AF: 0.247 AC: 37587 AN: 151942 Hom.: 4974 Cov.: 32 AF XY: 0.247 AC XY: 18354 AN XY: 74256

African (AFR) AF: 0.249 AC: 10308 AN: 41436

American (AMR) AF: 0.180 AC: 2751 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.148 AC: 514 AN: 3468

East Asian (EAS) AF: 0.331 AC: 1701 AN: 5146

South Asian (SAS) AF: 0.422 AC: 2030 AN: 4810

European-Finnish (FIN) AF: 0.224 AC: 2361 AN: 10538

Middle Eastern (MID) AF: 0.218 AC: 64 AN: 294

European-Non Finnish (NFE) AF: 0.251 AC: 17059 AN: 67956

Other (OTH) AF: 0.247 AC: 521 AN: 2110

Alfa AF: 0.245 Hom.: 8231

Bravo AF: 0.237

Asia WGS AF: 0.371 AC: 1293 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	2.0
DANN	Benign	0.60
PhyloP100		0.11

Splicing

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

Other links and lift over

dbSNP: rs7537266; hg19: chr1-238391155;