rs1202524

chr1-230815426-G-Achr1-230815426-G-Cchr1-230815426-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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;