rs1023102

Variant names:

• chr13-73250879-A-G
• rs1023102

Your query was ambiguous. Multiple possible variants found:

• chr13-73250879-A-G
• chr13-73250879-A-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 0.474 in 151,938 control chromosomes in the GnomAD database, including 17,279 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 (17279 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.44

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.578 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: 0.474 AC: 71949 AN: 151820 Hom.: 17258 Cov.: 31

Gnomad AFR AF: 0.466

Gnomad AMI AF: 0.378

Gnomad AMR AF: 0.549

Gnomad ASJ AF: 0.480

Gnomad EAS AF: 0.587

Gnomad SAS AF: 0.596

Gnomad FIN AF: 0.398

Gnomad MID AF: 0.497

Gnomad NFE AF: 0.457

Gnomad OTH AF: 0.475

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

GnomAD4 genome AF: 0.474 AC: 72008 AN: 151938 Hom.: 17279 Cov.: 31 AF XY: 0.476 AC XY: 35311 AN XY: 74250

Gnomad4 AFR AF: 0.466

Gnomad4 AMR AF: 0.550

Gnomad4 ASJ AF: 0.480

Gnomad4 EAS AF: 0.588

Gnomad4 SAS AF: 0.597

Gnomad4 FIN AF: 0.398

Gnomad4 NFE AF: 0.457

Gnomad4 OTH AF: 0.479

Alfa AF: 0.467 Hom.: 10337

Bravo AF: 0.485

Asia WGS AF: 0.612 AC: 2132 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	7.3
DANN	Benign	0.78

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1023102; hg19: chr13-73825016;