rs1202524

Variant names:

• chr1-230815426-G-A
• rs1202524

Your query was ambiguous. Multiple possible variants found:

• chr1-230815426-G-A
• chr1-230815426-G-C
• chr1-230815426-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 0.776 in 152,182 control chromosomes in the GnomAD database, including 46,575 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 0.78 (46575 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.777

ACMG classification

Verdict is Benign. Variant got -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 = 0.913 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: 0.776 AC: 117929 AN: 152064 Hom.: 46526 Cov.: 32

Gnomad AFR AF: 0.920

Gnomad AMI AF: 0.557

Gnomad AMR AF: 0.745

Gnomad ASJ AF: 0.779

Gnomad EAS AF: 0.886

Gnomad SAS AF: 0.913

Gnomad FIN AF: 0.708

Gnomad MID AF: 0.845

Gnomad NFE AF: 0.689

Gnomad OTH AF: 0.761

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

GnomAD4 genome AF: 0.776 AC: 118037 AN: 152182 Hom.: 46575 Cov.: 32 AF XY: 0.780 AC XY: 58003 AN XY: 74402

Gnomad4 AFR AF: 0.921

Gnomad4 AMR AF: 0.745

Gnomad4 ASJ AF: 0.779

Gnomad4 EAS AF: 0.885

Gnomad4 SAS AF: 0.912

Gnomad4 FIN AF: 0.708

Gnomad4 NFE AF: 0.689

Gnomad4 OTH AF: 0.763

Alfa AF: 0.719 Hom.: 52941

Bravo AF: 0.781

Asia WGS AF: 0.899 AC: 3125 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.41
DANN	Benign	0.30

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1202524; hg19: chr1-230951172;