rs7534091

Variant names:

• chr1-118321993-A-G
• rs7534091

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 152,070 control chromosomes in the GnomAD database, including 4,587 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 (4587 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.340
• Publications: 27 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.62).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.352 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: 36373 AN: 151952 Hom.: 4592 Cov.: 31

Gnomad AFR AF: 0.177

Gnomad AMI AF: 0.200

Gnomad AMR AF: 0.263

Gnomad ASJ AF: 0.317

Gnomad EAS AF: 0.365

Gnomad SAS AF: 0.315

Gnomad FIN AF: 0.234

Gnomad MID AF: 0.266

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: 36366 AN: 152070 Hom.: 4587 Cov.: 31 AF XY: 0.240 AC XY: 17845 AN XY: 74338

African (AFR) AF: 0.177 AC: 7351 AN: 41486

American (AMR) AF: 0.262 AC: 4009 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.317 AC: 1100 AN: 3470

East Asian (EAS) AF: 0.366 AC: 1881 AN: 5142

South Asian (SAS) AF: 0.315 AC: 1517 AN: 4818

European-Finnish (FIN) AF: 0.234 AC: 2471 AN: 10580

Middle Eastern (MID) AF: 0.248 AC: 73 AN: 294

European-Non Finnish (NFE) AF: 0.254 AC: 17275 AN: 67984

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

Alfa AF: 0.248 Hom.: 7965

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	-0.62
CADD	Benign	6.1
DANN	Benign	0.86
PhyloP100		0.34

Splicing

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

Other links and lift over

dbSNP: rs7534091; hg19: chr1-118864616;