chr10-112881038-T-A

Variant names:

• chr10-112881038-T-A
• rs10885390

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 0.294 in 152,098 control chromosomes in the GnomAD database, including 6,994 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 0.29 (6994 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.438
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.34 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: 0.295 AC: 44766 AN: 151980 Hom.: 6990 Cov.: 32

Gnomad AFR AF: 0.345

Gnomad AMI AF: 0.297

Gnomad AMR AF: 0.243

Gnomad ASJ AF: 0.347

Gnomad EAS AF: 0.00211

Gnomad SAS AF: 0.198

Gnomad FIN AF: 0.299

Gnomad MID AF: 0.345

Gnomad NFE AF: 0.301

Gnomad OTH AF: 0.313

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

GnomAD4 genome AF: 0.294 AC: 44790 AN: 152098 Hom.: 6994 Cov.: 32 AF XY: 0.292 AC XY: 21712 AN XY: 74350

African (AFR) AF: 0.344 AC: 14286 AN: 41470

American (AMR) AF: 0.243 AC: 3706 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.347 AC: 1202 AN: 3468

East Asian (EAS) AF: 0.00212 AC: 11 AN: 5192

South Asian (SAS) AF: 0.198 AC: 955 AN: 4822

European-Finnish (FIN) AF: 0.299 AC: 3162 AN: 10572

Middle Eastern (MID) AF: 0.347 AC: 102 AN: 294

European-Non Finnish (NFE) AF: 0.301 AC: 20440 AN: 67986

Other (OTH) AF: 0.310 AC: 656 AN: 2114

Alfa AF: 0.293 Hom.: 844

Bravo AF: 0.291

Asia WGS AF: 0.0940 AC: 330 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	3.4
DANN	Benign	0.46
PhyloP100		0.44

Splicing

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

Other links and lift over

dbSNP: rs10885390; hg19: chr10-114640797;