10-114054633-C-T

Variant names:

• chr10-114054633-C-T
• rs10885531
• ENST00000804402.1:n.194-7438G>A

Variant summary

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

The ENST00000804402.1(ENSG00000304538):​n.194-7438G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.429 in 151,844 control chromosomes in the GnomAD database, including 15,358 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 0.43 (15358 hom., cov: 31)
• Consequence: ENSG00000304538 ENST00000804402.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.899
• Publications: 15 publications found

Genes affected

ENSG00000304538 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.594 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC124902554	XR_007062383.1	n.194-7438G>A		intron_variant	Intron 1 of 1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000304538	ENST00000804402.1	n.194-7438G>A		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.429 AC: 65129 AN: 151726 Hom.: 15362 Cov.: 31

Gnomad AFR AF: 0.221

Gnomad AMI AF: 0.498

Gnomad AMR AF: 0.465

Gnomad ASJ AF: 0.465

Gnomad EAS AF: 0.613

Gnomad SAS AF: 0.560

Gnomad FIN AF: 0.551

Gnomad MID AF: 0.478

Gnomad NFE AF: 0.503

Gnomad OTH AF: 0.434

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

GnomAD4 genome AF: 0.429 AC: 65140 AN: 151844 Hom.: 15358 Cov.: 31 AF XY: 0.436 AC XY: 32348 AN XY: 74178

African (AFR) AF: 0.221 AC: 9145 AN: 41406

American (AMR) AF: 0.465 AC: 7087 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.465 AC: 1613 AN: 3466

East Asian (EAS) AF: 0.612 AC: 3146 AN: 5140

South Asian (SAS) AF: 0.561 AC: 2699 AN: 4812

European-Finnish (FIN) AF: 0.551 AC: 5805 AN: 10528

Middle Eastern (MID) AF: 0.473 AC: 139 AN: 294

European-Non Finnish (NFE) AF: 0.503 AC: 34145 AN: 67930

Other (OTH) AF: 0.432 AC: 909 AN: 2104

Alfa AF: 0.480 Hom.: 60344

Bravo AF: 0.409

Asia WGS AF: 0.524 AC: 1822 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.23
DANN	Benign	0.68
PhyloP100		-0.90

Splicing

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

Other links and lift over

dbSNP: rs10885531; hg19: chr10-115814392;