10-73942097-A-G

Position:

• chr10-73942097-A-G

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 0.406 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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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

Gnomad4 AFR AF: 0.565

Gnomad4 AMR AF: 0.517

Gnomad4 ASJ AF: 0.388

Gnomad4 EAS AF: 0.654

Gnomad4 SAS AF: 0.374

Gnomad4 FIN AF: 0.237

Gnomad4 NFE AF: 0.298

Gnomad4 OTH AF: 0.398

Alfa AF: 0.334 Hom.: 8464

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4746158; hg19: chr10-75701855;