10-73935966-T-G

Variant names:

• chr10-73935966-T-G
• rs2688624

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 6 publications found

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.803 AC: 33333 AN: 41492

American (AMR) AF: 0.606 AC: 9250 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.897 AC: 3113 AN: 3472

East Asian (EAS) AF: 0.509 AC: 2631 AN: 5166

South Asian (SAS) AF: 0.601 AC: 2897 AN: 4822

European-Finnish (FIN) AF: 0.600 AC: 6344 AN: 10566

Middle Eastern (MID) AF: 0.898 AC: 264 AN: 294

European-Non Finnish (NFE) AF: 0.753 AC: 51206 AN: 67984

Other (OTH) AF: 0.770 AC: 1620 AN: 2104

Alfa AF: 0.700 Hom.: 8382

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
PhyloP100		-1.9

Splicing

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

Other links and lift over

dbSNP: rs2688624; hg19: chr10-75695724;