rs10885531

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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000804402.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000304538	ENST00000804402.1		n.194-7438G>A		intron	N/A

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 v4.9

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs10885531;

hg19: chr10-115814392;