10-8108750-C-A

Variant names:

• chr10-8108750-C-A
• rs10508343
• ENST00000756604.1:n.92-198C>A

Variant summary

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

The ENST00000756604.1(ENSG00000298566):​n.92-198C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.022 in 152,060 control chromosomes in the GnomAD database, including 310 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 0.022 (310 hom., cov: 32)
• Consequence: ENSG00000298566 ENST00000756604.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.12
• Publications: 9 publications found

Genes affected

ENSG00000298566 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.144 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000756604.1. 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
	ENSG00000298566	ENST00000756604.1		n.92-198C>A		intron	N/A
	ENSG00000298566	ENST00000756605.1		n.79-2993C>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0219 AC: 3330 AN: 151942 Hom.: 305 Cov.: 32

Gnomad AFR AF: 0.00582

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.149

Gnomad ASJ AF: 0.000288

Gnomad EAS AF: 0.0630

Gnomad SAS AF: 0.0873

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.000382

Gnomad OTH AF: 0.0226

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

GnomAD4 genome AF: 0.0220 AC: 3345 AN: 152060 Hom.: 310 Cov.: 32 AF XY: 0.0252 AC XY: 1876 AN XY: 74350

African (AFR) AF: 0.00581 AC: 241 AN: 41498

American (AMR) AF: 0.149 AC: 2271 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.000288 AC: 1 AN: 3468

East Asian (EAS) AF: 0.0629 AC: 326 AN: 5180

South Asian (SAS) AF: 0.0880 AC: 424 AN: 4820

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 10536

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 294

European-Non Finnish (NFE) AF: 0.000383 AC: 26 AN: 67966

Other (OTH) AF: 0.0266 AC: 56 AN: 2104

Alfa AF: 0.00981 Hom.: 277

Bravo AF: 0.0346

Asia WGS AF: 0.0610 AC: 212 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.40
DANN	Benign	0.37
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs10508343; hg19: chr10-8150713;