10-42952399-A-G

Variant names:

• chr10-42952399-A-G
• rs2506030
• ENST00000736851.1:n.113-26A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000736851.1(ENSG00000296148):​n.113-26A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.355 in 152,140 control chromosomes in the GnomAD database, including 11,203 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 0.36 (11203 hom., cov: 33)
• Consequence: ENSG00000296148 ENST00000736851.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.437
• Publications: 35 publications found

Genes affected

ENSG00000296148 (HGNC:):

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 (EAS) allele frequency at 95% confidence interval = 0.696 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
ENSG00000296148	ENST00000736851.1	n.113-26A>G		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.356 AC: 54056 AN: 152022 Hom.: 11204 Cov.: 33

Gnomad AFR AF: 0.160

Gnomad AMI AF: 0.521

Gnomad AMR AF: 0.477

Gnomad ASJ AF: 0.455

Gnomad EAS AF: 0.716

Gnomad SAS AF: 0.536

Gnomad FIN AF: 0.405

Gnomad MID AF: 0.465

Gnomad NFE AF: 0.390

Gnomad OTH AF: 0.397

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

GnomAD4 genome AF: 0.355 AC: 54056 AN: 152140 Hom.: 11203 Cov.: 33 AF XY: 0.365 AC XY: 27120 AN XY: 74370

African (AFR) AF: 0.160 AC: 6626 AN: 41514

American (AMR) AF: 0.477 AC: 7297 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.455 AC: 1578 AN: 3470

East Asian (EAS) AF: 0.716 AC: 3697 AN: 5166

South Asian (SAS) AF: 0.536 AC: 2585 AN: 4824

European-Finnish (FIN) AF: 0.405 AC: 4285 AN: 10584

Middle Eastern (MID) AF: 0.459 AC: 135 AN: 294

European-Non Finnish (NFE) AF: 0.390 AC: 26530 AN: 67966

Other (OTH) AF: 0.401 AC: 848 AN: 2114

Alfa AF: 0.376 Hom.: 20666

Bravo AF: 0.352

Asia WGS AF: 0.569 AC: 1973 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	1.6
DANN	Benign	0.37
PhyloP100		-0.44

Splicing

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

Other links and lift over

dbSNP: rs2506030; hg19: chr10-43447847;