chr10-44355202-G-A

Variant names:

• chr10-44355202-G-A
• rs1147879

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 0.421 in 152,006 control chromosomes in the GnomAD database, including 14,573 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 0.42 (14573 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.73
• Publications: 7 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.608 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: 0.421 AC: 63992 AN: 151888 Hom.: 14565 Cov.: 32

Gnomad AFR AF: 0.237

Gnomad AMI AF: 0.682

Gnomad AMR AF: 0.415

Gnomad ASJ AF: 0.477

Gnomad EAS AF: 0.627

Gnomad SAS AF: 0.437

Gnomad FIN AF: 0.454

Gnomad MID AF: 0.427

Gnomad NFE AF: 0.506

Gnomad OTH AF: 0.427

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

GnomAD4 genome AF: 0.421 AC: 64010 AN: 152006 Hom.: 14573 Cov.: 32 AF XY: 0.418 AC XY: 31070 AN XY: 74288

African (AFR) AF: 0.237 AC: 9837 AN: 41482

American (AMR) AF: 0.415 AC: 6341 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.477 AC: 1656 AN: 3470

East Asian (EAS) AF: 0.626 AC: 3224 AN: 5148

South Asian (SAS) AF: 0.436 AC: 2101 AN: 4820

European-Finnish (FIN) AF: 0.454 AC: 4785 AN: 10546

Middle Eastern (MID) AF: 0.418 AC: 123 AN: 294

European-Non Finnish (NFE) AF: 0.506 AC: 34406 AN: 67950

Other (OTH) AF: 0.435 AC: 919 AN: 2112

Alfa AF: 0.465 Hom.: 9340

Bravo AF: 0.411

Asia WGS AF: 0.543 AC: 1884 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	0.058
DANN	Benign	0.29
PhyloP100		-1.7
Mutation Taster		=100/0	polymorphism (auto)

Splicing

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

Other links and lift over

dbSNP: rs1147879; hg19: chr10-44850650;