rs10491110

Variant names:

• chr17-34221498-T-C
• rs10491110
• ENST00000776537.1:n.239-2077A>G

Variant summary

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

The ENST00000776537.1(ENSG00000301139):​n.239-2077A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.125 in 152,176 control chromosomes in the GnomAD database, including 1,699 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 0.12 (1699 hom., cov: 33)
• Consequence: ENSG00000301139 ENST00000776537.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.05
• Publications: 5 publications found

Genes affected

ENSG00000301139 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.244 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000301139	ENST00000776537.1	n.239-2077A>G		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.124 AC: 18885 AN: 152058 Hom.: 1678 Cov.: 33

Gnomad AFR AF: 0.248

Gnomad AMI AF: 0.187

Gnomad AMR AF: 0.0860

Gnomad ASJ AF: 0.0620

Gnomad EAS AF: 0.136

Gnomad SAS AF: 0.192

Gnomad FIN AF: 0.0539

Gnomad MID AF: 0.0949

Gnomad NFE AF: 0.0657

Gnomad OTH AF: 0.117

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

GnomAD4 genome AF: 0.125 AC: 18955 AN: 152176 Hom.: 1699 Cov.: 33 AF XY: 0.125 AC XY: 9305 AN XY: 74414

African (AFR) AF: 0.248 AC: 10303 AN: 41488

American (AMR) AF: 0.0858 AC: 1311 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.0620 AC: 215 AN: 3468

East Asian (EAS) AF: 0.136 AC: 702 AN: 5174

South Asian (SAS) AF: 0.192 AC: 926 AN: 4826

European-Finnish (FIN) AF: 0.0539 AC: 572 AN: 10614

Middle Eastern (MID) AF: 0.0952 AC: 28 AN: 294

European-Non Finnish (NFE) AF: 0.0657 AC: 4468 AN: 68016

Other (OTH) AF: 0.123 AC: 260 AN: 2106

Alfa AF: 0.0977 Hom.: 180

Bravo AF: 0.129

Asia WGS AF: 0.187 AC: 649 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	0.14
DANN	Benign	0.60
PhyloP100		-2.0

Splicing

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

Other links and lift over

dbSNP: rs10491110; hg19: chr17-32548517;