rs7536458

Variant names:

• chr1-118321979-T-G
• rs7536458

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 0.239 in 152,064 control chromosomes in the GnomAD database, including 4,591 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 0.24 (4591 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0320
• Publications: 18 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.73).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.353 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: 0.239 AC: 36389 AN: 151946 Hom.: 4596 Cov.: 31

Gnomad AFR AF: 0.178

Gnomad AMI AF: 0.200

Gnomad AMR AF: 0.263

Gnomad ASJ AF: 0.317

Gnomad EAS AF: 0.367

Gnomad SAS AF: 0.316

Gnomad FIN AF: 0.234

Gnomad MID AF: 0.263

Gnomad NFE AF: 0.254

Gnomad OTH AF: 0.243

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

GnomAD4 genome AF: 0.239 AC: 36382 AN: 152064 Hom.: 4591 Cov.: 31 AF XY: 0.240 AC XY: 17855 AN XY: 74324

African (AFR) AF: 0.177 AC: 7359 AN: 41496

American (AMR) AF: 0.262 AC: 4004 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.317 AC: 1101 AN: 3468

East Asian (EAS) AF: 0.367 AC: 1892 AN: 5154

South Asian (SAS) AF: 0.315 AC: 1518 AN: 4816

European-Finnish (FIN) AF: 0.234 AC: 2471 AN: 10566

Middle Eastern (MID) AF: 0.245 AC: 72 AN: 294

European-Non Finnish (NFE) AF: 0.254 AC: 17276 AN: 67988

Other (OTH) AF: 0.241 AC: 507 AN: 2108

Alfa AF: 0.250 Hom.: 17120

Bravo AF: 0.237

Asia WGS AF: 0.303 AC: 1051 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.73
CADD	Benign	6.2
DANN	Benign	0.78
PhyloP100		0.032

Splicing

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

Other links and lift over

dbSNP: rs7536458; hg19: chr1-118864602; COSMIC: COSV107159785;