rs7524281

Variant names:

• chr1-152810779-C-A
• rs7524281

Your query was ambiguous. Multiple possible variants found:

• chr1-152810779-C-A
• chr1-152810779-C-G
• chr1-152810779-C-T

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 0.408 in 152,032 control chromosomes in the GnomAD database, including 13,504 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 0.41 (13504 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.902
• Publications: 13 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.567 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: 0.407 AC: 61892 AN: 151916 Hom.: 13478 Cov.: 33

Gnomad AFR AF: 0.573

Gnomad AMI AF: 0.265

Gnomad AMR AF: 0.393

Gnomad ASJ AF: 0.314

Gnomad EAS AF: 0.286

Gnomad SAS AF: 0.302

Gnomad FIN AF: 0.305

Gnomad MID AF: 0.449

Gnomad NFE AF: 0.349

Gnomad OTH AF: 0.391

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

GnomAD4 genome AF: 0.408 AC: 61964 AN: 152032 Hom.: 13504 Cov.: 33 AF XY: 0.405 AC XY: 30089 AN XY: 74324

African (AFR) AF: 0.574 AC: 23776 AN: 41454

American (AMR) AF: 0.393 AC: 6009 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.314 AC: 1090 AN: 3466

East Asian (EAS) AF: 0.286 AC: 1483 AN: 5180

South Asian (SAS) AF: 0.302 AC: 1455 AN: 4820

European-Finnish (FIN) AF: 0.305 AC: 3227 AN: 10566

Middle Eastern (MID) AF: 0.445 AC: 130 AN: 292

European-Non Finnish (NFE) AF: 0.349 AC: 23733 AN: 67938

Other (OTH) AF: 0.387 AC: 819 AN: 2114

Alfa AF: 0.361 Hom.: 17298

Bravo AF: 0.422

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.27
DANN	Benign	0.28
PhyloP100		-0.90

Splicing

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

Other links and lift over

dbSNP: rs7524281; hg19: chr1-152783255;