10-101214115-A-G

Variant names:

• chr10-101214115-A-G
• rs1535462

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 0.497 in 148,658 control chromosomes in the GnomAD database, including 18,987 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 0.50 (18987 hom., cov: 25)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.20

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.621 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: 0.497 AC: 73872 AN: 148570 Hom.: 18956 Cov.: 25

Gnomad AFR AF: 0.627

Gnomad AMI AF: 0.347

Gnomad AMR AF: 0.395

Gnomad ASJ AF: 0.455

Gnomad EAS AF: 0.581

Gnomad SAS AF: 0.333

Gnomad FIN AF: 0.401

Gnomad MID AF: 0.381

Gnomad NFE AF: 0.466

Gnomad OTH AF: 0.474

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

GnomAD4 genome AF: 0.497 AC: 73951 AN: 148658 Hom.: 18987 Cov.: 25 AF XY: 0.490 AC XY: 35398 AN XY: 72292

Gnomad4 AFR AF: 0.628

Gnomad4 AMR AF: 0.395

Gnomad4 ASJ AF: 0.455

Gnomad4 EAS AF: 0.581

Gnomad4 SAS AF: 0.334

Gnomad4 FIN AF: 0.401

Gnomad4 NFE AF: 0.466

Gnomad4 OTH AF: 0.475

Alfa AF: 0.313 Hom.: 740

Bravo AF: 0.506

Asia WGS AF: 0.430 AC: 1483 AN: 3460

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	3.1
DANN	Benign	0.12

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1535462; hg19: chr10-102973872;