chr10-73942097-A-G

Variant names:

• chr10-73942097-A-G
• rs4746158

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 0.406 in 152,110 control chromosomes in the GnomAD database, including 14,028 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 0.41 (14028 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.827
• Publications: 6 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.635 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: 0.406 AC: 61671 AN: 151992 Hom.: 13993 Cov.: 32

Gnomad AFR AF: 0.565

Gnomad AMI AF: 0.151

Gnomad AMR AF: 0.516

Gnomad ASJ AF: 0.388

Gnomad EAS AF: 0.653

Gnomad SAS AF: 0.375

Gnomad FIN AF: 0.237

Gnomad MID AF: 0.402

Gnomad NFE AF: 0.298

Gnomad OTH AF: 0.398

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

GnomAD4 genome AF: 0.406 AC: 61764 AN: 152110 Hom.: 14028 Cov.: 32 AF XY: 0.405 AC XY: 30130 AN XY: 74370

African (AFR) AF: 0.565 AC: 23447 AN: 41470

American (AMR) AF: 0.517 AC: 7892 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.388 AC: 1345 AN: 3470

East Asian (EAS) AF: 0.654 AC: 3383 AN: 5176

South Asian (SAS) AF: 0.374 AC: 1805 AN: 4824

European-Finnish (FIN) AF: 0.237 AC: 2510 AN: 10584

Middle Eastern (MID) AF: 0.398 AC: 117 AN: 294

European-Non Finnish (NFE) AF: 0.298 AC: 20290 AN: 68004

Other (OTH) AF: 0.398 AC: 837 AN: 2104

Alfa AF: 0.335 Hom.: 10123

Bravo AF: 0.434

Asia WGS AF: 0.504 AC: 1750 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.037
DANN	Benign	0.17
PhyloP100		-0.83

Splicing

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

Other links and lift over

dbSNP: rs4746158; hg19: chr10-75701855;