10-87652818-G-T

Variant names:

• chr10-87652818-G-T
• rs791888
• ENST00000354527.2:n.146+7040C>A

Variant summary

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

The ENST00000354527.2(ENSG00000196566):​n.146+7040C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.356 in 151,904 control chromosomes in the GnomAD database, including 10,162 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 (10162 hom., cov: 32)
• Consequence: ENSG00000196566 ENST00000354527.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.911
• Publications: 11 publications found

Genes affected

ENSG00000196566 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.428 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000354527.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000196566	ENST00000354527.2	TSL:3	n.146+7040C>A		intron	N/A
	ENSG00000225913	ENST00000438082.1	TSL:3	n.109-5685G>T		intron	N/A
	ENSG00000225913	ENST00000804457.1		n.214-2203G>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.356 AC: 54106 AN: 151786 Hom.: 10157 Cov.: 32

Gnomad AFR AF: 0.285

Gnomad AMI AF: 0.327

Gnomad AMR AF: 0.352

Gnomad ASJ AF: 0.369

Gnomad EAS AF: 0.129

Gnomad SAS AF: 0.291

Gnomad FIN AF: 0.294

Gnomad MID AF: 0.421

Gnomad NFE AF: 0.432

Gnomad OTH AF: 0.369

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

GnomAD4 genome AF: 0.356 AC: 54151 AN: 151904 Hom.: 10162 Cov.: 32 AF XY: 0.347 AC XY: 25734 AN XY: 74242

African (AFR) AF: 0.285 AC: 11823 AN: 41424

American (AMR) AF: 0.352 AC: 5370 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.369 AC: 1278 AN: 3468

East Asian (EAS) AF: 0.129 AC: 669 AN: 5174

South Asian (SAS) AF: 0.290 AC: 1394 AN: 4808

European-Finnish (FIN) AF: 0.294 AC: 3090 AN: 10520

Middle Eastern (MID) AF: 0.422 AC: 124 AN: 294

European-Non Finnish (NFE) AF: 0.432 AC: 29326 AN: 67932

Other (OTH) AF: 0.369 AC: 779 AN: 2112

Alfa AF: 0.412 Hom.: 22240

Bravo AF: 0.361

Asia WGS AF: 0.221 AC: 770 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	9.6
DANN	Benign	0.69
PhyloP100		0.91

Splicing

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

Other links and lift over

dbSNP: rs791888; hg19: chr10-89412575;