10-72051156-G-C

Position:

• chr10-72051156-G-C

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 0.39 in 152,098 control chromosomes in the GnomAD database, including 12,539 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 0.39 (12539 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.439

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.482 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: 0.391 AC: 59380 AN: 151980 Hom.: 12540 Cov.: 32

Gnomad AFR AF: 0.252

Gnomad AMI AF: 0.493

Gnomad AMR AF: 0.393

Gnomad ASJ AF: 0.510

Gnomad EAS AF: 0.116

Gnomad SAS AF: 0.293

Gnomad FIN AF: 0.436

Gnomad MID AF: 0.478

Gnomad NFE AF: 0.486

Gnomad OTH AF: 0.440

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

GnomAD4 genome AF: 0.390 AC: 59379 AN: 152098 Hom.: 12539 Cov.: 32 AF XY: 0.383 AC XY: 28476 AN XY: 74332

Gnomad4 AFR AF: 0.252

Gnomad4 AMR AF: 0.393

Gnomad4 ASJ AF: 0.510

Gnomad4 EAS AF: 0.115

Gnomad4 SAS AF: 0.293

Gnomad4 FIN AF: 0.436

Gnomad4 NFE AF: 0.486

Gnomad4 OTH AF: 0.433

Alfa AF: 0.289 Hom.: 749

Bravo AF: 0.381

Asia WGS AF: 0.206 AC: 721 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.094
DANN	Benign	0.39

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1245577; hg19: chr10-73810914;