rs7523412

Variant names:

• chr1-24967773-G-A
• rs7523412

Your query was ambiguous. Multiple possible variants found:

• chr1-24967773-G-A
• chr1-24967773-G-C
• chr1-24967773-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 0.471 in 152,022 control chromosomes in the GnomAD database, including 18,317 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 0.47 (18317 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.707
• Publications: 11 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.689 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.471 AC: 71622 AN: 151904 Hom.: 18288 Cov.: 32

Gnomad AFR AF: 0.278

Gnomad AMI AF: 0.690

Gnomad AMR AF: 0.638

Gnomad ASJ AF: 0.509

Gnomad EAS AF: 0.708

Gnomad SAS AF: 0.669

Gnomad FIN AF: 0.575

Gnomad MID AF: 0.528

Gnomad NFE AF: 0.497

Gnomad OTH AF: 0.504

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

GnomAD4 genome AF: 0.471 AC: 71670 AN: 152022 Hom.: 18317 Cov.: 32 AF XY: 0.487 AC XY: 36165 AN XY: 74300

African (AFR) AF: 0.278 AC: 11503 AN: 41418

American (AMR) AF: 0.639 AC: 9758 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.509 AC: 1767 AN: 3470

East Asian (EAS) AF: 0.708 AC: 3660 AN: 5172

South Asian (SAS) AF: 0.670 AC: 3226 AN: 4818

European-Finnish (FIN) AF: 0.575 AC: 6073 AN: 10560

Middle Eastern (MID) AF: 0.531 AC: 156 AN: 294

European-Non Finnish (NFE) AF: 0.497 AC: 33822 AN: 67988

Other (OTH) AF: 0.510 AC: 1077 AN: 2112

Alfa AF: 0.493 Hom.: 21512

Bravo AF: 0.468

Asia WGS AF: 0.691 AC: 2403 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	4.2
DANN	Benign	0.60
PhyloP100		0.71

Splicing

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

Other links and lift over

dbSNP: rs7523412; hg19: chr1-25294264;