13-102977121-A-G

Variant names:

• chr13-102977121-A-G
• rs10508097

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 0.0241 in 152,334 control chromosomes in the GnomAD database, including 65 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 0.024 (65 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.439

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.6).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.061 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: 0.0241 AC: 3668 AN: 152216 Hom.: 63 Cov.: 32

Gnomad AFR AF: 0.00593

Gnomad AMI AF: 0.0625

Gnomad AMR AF: 0.0207

Gnomad ASJ AF: 0.0821

Gnomad EAS AF: 0.00115

Gnomad SAS AF: 0.0658

Gnomad FIN AF: 0.00998

Gnomad MID AF: 0.0506

Gnomad NFE AF: 0.0331

Gnomad OTH AF: 0.0306

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

GnomAD4 genome AF: 0.0241 AC: 3674 AN: 152334 Hom.: 65 Cov.: 32 AF XY: 0.0231 AC XY: 1724 AN XY: 74500

Gnomad4 AFR AF: 0.00594

Gnomad4 AMR AF: 0.0207

Gnomad4 ASJ AF: 0.0821

Gnomad4 EAS AF: 0.00116

Gnomad4 SAS AF: 0.0671

Gnomad4 FIN AF: 0.00998

Gnomad4 NFE AF: 0.0331

Gnomad4 OTH AF: 0.0298

Alfa AF: 0.0269 Hom.: 2

Bravo AF: 0.0240

Asia WGS AF: 0.0210 AC: 74 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.60
CADD	Benign	3.5
DANN	Benign	0.71

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10508097; hg19: chr13-103629471;