rs7524769

Variant names:

• chr1-165044298-G-A
• rs7524769

Your query was ambiguous. Multiple possible variants found:

• chr1-165044298-G-A
• chr1-165044298-G-C
• chr1-165044298-G-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 0.402 in 151,936 control chromosomes in the GnomAD database, including 12,804 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 0.40 (12804 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.78
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.542 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: 0.402 AC: 61021 AN: 151820 Hom.: 12778 Cov.: 32

Gnomad AFR AF: 0.379

Gnomad AMI AF: 0.293

Gnomad AMR AF: 0.551

Gnomad ASJ AF: 0.441

Gnomad EAS AF: 0.527

Gnomad SAS AF: 0.545

Gnomad FIN AF: 0.342

Gnomad MID AF: 0.433

Gnomad NFE AF: 0.371

Gnomad OTH AF: 0.414

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

GnomAD4 genome AF: 0.402 AC: 61099 AN: 151936 Hom.: 12804 Cov.: 32 AF XY: 0.408 AC XY: 30255 AN XY: 74236

African (AFR) AF: 0.379 AC: 15702 AN: 41434

American (AMR) AF: 0.552 AC: 8427 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.441 AC: 1529 AN: 3464

East Asian (EAS) AF: 0.527 AC: 2710 AN: 5144

South Asian (SAS) AF: 0.545 AC: 2626 AN: 4818

European-Finnish (FIN) AF: 0.342 AC: 3607 AN: 10546

Middle Eastern (MID) AF: 0.442 AC: 129 AN: 292

European-Non Finnish (NFE) AF: 0.371 AC: 25216 AN: 67946

Other (OTH) AF: 0.420 AC: 886 AN: 2112

Alfa AF: 0.391 Hom.: 39091

Bravo AF: 0.417

Asia WGS AF: 0.550 AC: 1913 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.011
DANN	Benign	0.54
PhyloP100		-1.8

Splicing

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

Other links and lift over

dbSNP: rs7524769; hg19: chr1-165013535;