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. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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.

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: 0.471 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

Gnomad4 AFR AF: 0.278

Gnomad4 AMR AF: 0.639

Gnomad4 ASJ AF: 0.509

Gnomad4 EAS AF: 0.708

Gnomad4 SAS AF: 0.670

Gnomad4 FIN AF: 0.575

Gnomad4 NFE AF: 0.497

Gnomad4 OTH AF: 0.510

Alfa AF: 0.499 Hom.: 14369

Bravo AF: 0.468

Asia WGS AF: 0.691 AC: 2403 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7523412; hg19: chr1-25294264;