10-73886389-A-T

Variant names:

• chr10-73886389-A-T
• rs2688617

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 0.723 in 152,082 control chromosomes in the GnomAD database, including 40,438 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 0.72 (40438 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.325

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 (AFR) allele frequency at 95% confidence interval = 0.758 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: 0.723 AC: 109909 AN: 151964 Hom.: 40415 Cov.: 32

Gnomad AFR AF: 0.766

Gnomad AMI AF: 0.685

Gnomad AMR AF: 0.596

Gnomad ASJ AF: 0.907

Gnomad EAS AF: 0.481

Gnomad SAS AF: 0.604

Gnomad FIN AF: 0.630

Gnomad MID AF: 0.861

Gnomad NFE AF: 0.756

Gnomad OTH AF: 0.776

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

GnomAD4 genome AF: 0.723 AC: 109964 AN: 152082 Hom.: 40438 Cov.: 32 AF XY: 0.714 AC XY: 53036 AN XY: 74320

Gnomad4 AFR AF: 0.765

Gnomad4 AMR AF: 0.596

Gnomad4 ASJ AF: 0.907

Gnomad4 EAS AF: 0.481

Gnomad4 SAS AF: 0.604

Gnomad4 FIN AF: 0.630

Gnomad4 NFE AF: 0.756

Gnomad4 OTH AF: 0.768

Alfa AF: 0.732 Hom.: 5090

Bravo AF: 0.724

Asia WGS AF: 0.518 AC: 1807 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	1.9
DANN	Benign	0.51

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2688617; hg19: chr10-75646147;