chr10-103927874-A-C

Variant names:

• chr10-103927874-A-C
• rs11591710
• ENST00000698239.1:n.274-10218T>G

Variant summary

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

The ENST00000698239.1(ENSG00000289744):​n.274-10218T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.161 in 152,136 control chromosomes in the GnomAD database, including 2,352 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 0.16 (2352 hom., cov: 32)
• Consequence: ENSG00000289744 ENST00000698239.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.650
• Publications: 20 publications found

Genes affected

ENSG00000289744 (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 (AFR) allele frequency at 95% confidence interval = 0.256 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000698239.1. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000289744	ENST00000698239.1		n.274-10218T>G		intron	N/A
	ENSG00000289744	ENST00000698240.1		n.389-10218T>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.161 AC: 24412 AN: 152018 Hom.: 2336 Cov.: 32

Gnomad AFR AF: 0.260

Gnomad AMI AF: 0.0482

Gnomad AMR AF: 0.109

Gnomad ASJ AF: 0.167

Gnomad EAS AF: 0.0127

Gnomad SAS AF: 0.0901

Gnomad FIN AF: 0.113

Gnomad MID AF: 0.136

Gnomad NFE AF: 0.137

Gnomad OTH AF: 0.153

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

GnomAD4 genome AF: 0.161 AC: 24468 AN: 152136 Hom.: 2352 Cov.: 32 AF XY: 0.156 AC XY: 11632 AN XY: 74390

African (AFR) AF: 0.260 AC: 10789 AN: 41446

American (AMR) AF: 0.109 AC: 1659 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.167 AC: 580 AN: 3470

East Asian (EAS) AF: 0.0131 AC: 68 AN: 5188

South Asian (SAS) AF: 0.0891 AC: 430 AN: 4824

European-Finnish (FIN) AF: 0.113 AC: 1193 AN: 10598

Middle Eastern (MID) AF: 0.139 AC: 41 AN: 294

European-Non Finnish (NFE) AF: 0.137 AC: 9330 AN: 68006

Other (OTH) AF: 0.158 AC: 334 AN: 2110

Alfa AF: 0.149 Hom.: 231

Bravo AF: 0.164

Asia WGS AF: 0.112 AC: 388 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	4.1
DANN	Benign	0.43
PhyloP100		0.65

Splicing

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

Other links and lift over

dbSNP: rs11591710; hg19: chr10-105687632;