rs7534480

Variant names:

• chr1-182590218-C-T
• rs7534480

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 0.359 in 151,980 control chromosomes in the GnomAD database, including 9,917 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 0.36 (9917 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0200
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.391 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: 0.359 AC: 54555 AN: 151862 Hom.: 9916 Cov.: 31

Gnomad AFR AF: 0.345

Gnomad AMI AF: 0.405

Gnomad AMR AF: 0.288

Gnomad ASJ AF: 0.297

Gnomad EAS AF: 0.237

Gnomad SAS AF: 0.298

Gnomad FIN AF: 0.396

Gnomad MID AF: 0.320

Gnomad NFE AF: 0.395

Gnomad OTH AF: 0.351

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

GnomAD4 genome AF: 0.359 AC: 54574 AN: 151980 Hom.: 9917 Cov.: 31 AF XY: 0.357 AC XY: 26508 AN XY: 74258

African (AFR) AF: 0.345 AC: 14288 AN: 41436

American (AMR) AF: 0.287 AC: 4389 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.297 AC: 1032 AN: 3470

East Asian (EAS) AF: 0.237 AC: 1227 AN: 5168

South Asian (SAS) AF: 0.297 AC: 1430 AN: 4808

European-Finnish (FIN) AF: 0.396 AC: 4174 AN: 10542

Middle Eastern (MID) AF: 0.306 AC: 90 AN: 294

European-Non Finnish (NFE) AF: 0.395 AC: 26831 AN: 67958

Other (OTH) AF: 0.352 AC: 744 AN: 2116

Alfa AF: 0.386 Hom.: 1433

Bravo AF: 0.348

Asia WGS AF: 0.305 AC: 1063 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	2.1
DANN	Benign	0.67
PhyloP100		0.020

Splicing

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

Other links and lift over

dbSNP: rs7534480; hg19: chr1-182559353;