10-73935966-T-G

Variant names:

• chr10-73935966-T-G
• rs2688624

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 0.732 in 152,066 control chromosomes in the GnomAD database, including 41,434 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 0.73 (41434 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.85

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.796 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: 0.732 AC: 111239 AN: 151948 Hom.: 41413 Cov.: 32

Gnomad AFR AF: 0.804

Gnomad AMI AF: 0.704

Gnomad AMR AF: 0.607

Gnomad ASJ AF: 0.897

Gnomad EAS AF: 0.508

Gnomad SAS AF: 0.600

Gnomad FIN AF: 0.600

Gnomad MID AF: 0.899

Gnomad NFE AF: 0.753

Gnomad OTH AF: 0.779

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

GnomAD4 genome AF: 0.732 AC: 111299 AN: 152066 Hom.: 41434 Cov.: 32 AF XY: 0.721 AC XY: 53590 AN XY: 74336

Gnomad4 AFR AF: 0.803

Gnomad4 AMR AF: 0.606

Gnomad4 ASJ AF: 0.897

Gnomad4 EAS AF: 0.509

Gnomad4 SAS AF: 0.601

Gnomad4 FIN AF: 0.600

Gnomad4 NFE AF: 0.753

Gnomad4 OTH AF: 0.770

Alfa AF: 0.633 Hom.: 1737

Bravo AF: 0.738

Asia WGS AF: 0.538 AC: 1875 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.049
DANN	Benign	0.54

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2688624; hg19: chr10-75695724;