10-43274443-A-G

Variant names:

• chr10-43274443-A-G
• rs2505526

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 0.13 in 152,234 control chromosomes in the GnomAD database, including 2,088 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 0.13 (2088 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.473
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.512 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: 0.130 AC: 19779 AN: 152116 Hom.: 2091 Cov.: 32

Gnomad AFR AF: 0.0367

Gnomad AMI AF: 0.0899

Gnomad AMR AF: 0.226

Gnomad ASJ AF: 0.165

Gnomad EAS AF: 0.529

Gnomad SAS AF: 0.260

Gnomad FIN AF: 0.109

Gnomad MID AF: 0.180

Gnomad NFE AF: 0.127

Gnomad OTH AF: 0.148

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

GnomAD4 genome AF: 0.130 AC: 19771 AN: 152234 Hom.: 2088 Cov.: 32 AF XY: 0.135 AC XY: 10034 AN XY: 74410

African (AFR) AF: 0.0366 AC: 1521 AN: 41564

American (AMR) AF: 0.226 AC: 3462 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.165 AC: 573 AN: 3472

East Asian (EAS) AF: 0.529 AC: 2721 AN: 5148

South Asian (SAS) AF: 0.258 AC: 1242 AN: 4812

European-Finnish (FIN) AF: 0.109 AC: 1158 AN: 10606

Middle Eastern (MID) AF: 0.177 AC: 52 AN: 294

European-Non Finnish (NFE) AF: 0.127 AC: 8648 AN: 68018

Other (OTH) AF: 0.148 AC: 312 AN: 2114

Alfa AF: 0.143 Hom.: 317

Bravo AF: 0.133

Asia WGS AF: 0.374 AC: 1296 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	2.1
DANN	Benign	0.80
PhyloP100		0.47

Splicing

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

Other links and lift over

dbSNP: rs2505526; hg19: chr10-43769891;