10-73903978-A-G

Variant names:

• chr10-73903978-A-G
• rs2688607

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 0.73 in 152,074 control chromosomes in the GnomAD database, including 41,258 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 (41258 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.948
• Publications: 15 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.788 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: 0.730 AC: 110963 AN: 151956 Hom.: 41219 Cov.: 32

Gnomad AFR AF: 0.795

Gnomad AMI AF: 0.702

Gnomad AMR AF: 0.599

Gnomad ASJ AF: 0.908

Gnomad EAS AF: 0.434

Gnomad SAS AF: 0.604

Gnomad FIN AF: 0.659

Gnomad MID AF: 0.848

Gnomad NFE AF: 0.753

Gnomad OTH AF: 0.764

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

GnomAD4 genome AF: 0.730 AC: 111042 AN: 152074 Hom.: 41258 Cov.: 32 AF XY: 0.721 AC XY: 53599 AN XY: 74338

African (AFR) AF: 0.795 AC: 32966 AN: 41470

American (AMR) AF: 0.599 AC: 9143 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.908 AC: 3154 AN: 3472

East Asian (EAS) AF: 0.434 AC: 2247 AN: 5180

South Asian (SAS) AF: 0.604 AC: 2912 AN: 4818

European-Finnish (FIN) AF: 0.659 AC: 6953 AN: 10552

Middle Eastern (MID) AF: 0.854 AC: 251 AN: 294

European-Non Finnish (NFE) AF: 0.753 AC: 51180 AN: 67988

Other (OTH) AF: 0.755 AC: 1597 AN: 2114

Alfa AF: 0.749 Hom.: 77848

Bravo AF: 0.731

Asia WGS AF: 0.492 AC: 1717 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.41
DANN	Benign	0.76
PhyloP100		-0.95

Splicing

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

Other links and lift over

dbSNP: rs2688607; hg19: chr10-75663736;