rs7534091

chr1-118321993-A-G

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 0.239 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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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

Gnomad4 AFR AF: 0.177

Gnomad4 AMR AF: 0.262

Gnomad4 ASJ AF: 0.317

Gnomad4 EAS AF: 0.366

Gnomad4 SAS AF: 0.315

Gnomad4 FIN AF: 0.234

Gnomad4 NFE AF: 0.254

Gnomad4 OTH AF: 0.241

Alfa AF: 0.234 Hom.: 617

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7534091; hg19: chr1-118864616;