rs10905651

Variant names:

• chr10-10031581-G-A
• rs10905651
• ENST00000738164.1:n.194+35514G>A

Variant summary

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

The ENST00000738164.1(ENSG00000296323):​n.194+35514G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.535 in 152,012 control chromosomes in the GnomAD database, including 22,291 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 0.53 (22291 hom., cov: 32)
• Consequence: ENSG00000296323 ENST00000738164.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.567
• Publications: 5 publications found

Genes affected

ENSG00000296323 (HGNC:):

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 (AFR) allele frequency at 95% confidence interval = 0.649 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
ENSG00000296323	ENST00000738164.1	n.194+35514G>A		intron_variant	Intron 2 of 8
ENSG00000296323	ENST00000738165.1	n.221+35514G>A		intron_variant	Intron 2 of 6

Frequencies

GnomAD3 genomes AF: 0.535 AC: 81226 AN: 151894 Hom.: 22270 Cov.: 32

Gnomad AFR AF: 0.655

Gnomad AMI AF: 0.436

Gnomad AMR AF: 0.517

Gnomad ASJ AF: 0.512

Gnomad EAS AF: 0.399

Gnomad SAS AF: 0.376

Gnomad FIN AF: 0.397

Gnomad MID AF: 0.579

Gnomad NFE AF: 0.510

Gnomad OTH AF: 0.543

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

GnomAD4 genome AF: 0.535 AC: 81288 AN: 152012 Hom.: 22291 Cov.: 32 AF XY: 0.527 AC XY: 39128 AN XY: 74278

African (AFR) AF: 0.655 AC: 27161 AN: 41456

American (AMR) AF: 0.517 AC: 7892 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.512 AC: 1777 AN: 3470

East Asian (EAS) AF: 0.400 AC: 2065 AN: 5166

South Asian (SAS) AF: 0.375 AC: 1805 AN: 4818

European-Finnish (FIN) AF: 0.397 AC: 4184 AN: 10528

Middle Eastern (MID) AF: 0.585 AC: 172 AN: 294

European-Non Finnish (NFE) AF: 0.510 AC: 34701 AN: 67990

Other (OTH) AF: 0.536 AC: 1133 AN: 2112

Alfa AF: 0.519 Hom.: 41355

Bravo AF: 0.555

Asia WGS AF: 0.381 AC: 1327 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	0.79
DANN	Benign	0.57
PhyloP100		-0.57

Splicing

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

Other links and lift over

dbSNP: rs10905651; hg19: chr10-10073544;