rs17109512

Variant names:

• chr10-98367794-G-A
• rs17109512
• ENST00000815097.1:n.411-401G>A

Variant summary

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

The ENST00000815097.1(ENSG00000306073):​n.411-401G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0944 in 151,986 control chromosomes in the GnomAD database, including 1,026 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 0.094 (1026 hom., cov: 32)
• Consequence: ENSG00000306073 ENST00000815097.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0790
• Publications: 14 publications found

Genes affected

ENSG00000306073 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.179 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105378449	XR_001747305.2	n.396-401G>A		intron_variant	Intron 2 of 2
LOC105378449	XR_946233.3	n.326-401G>A		intron_variant	Intron 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000306073	ENST00000815097.1	n.411-401G>A		intron_variant	Intron 2 of 2
ENSG00000306073	ENST00000815098.1	n.440-401G>A		intron_variant	Intron 2 of 2
ENSG00000306073	ENST00000815099.1	n.804-401G>A		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.0943 AC: 14327 AN: 151868 Hom.: 1023 Cov.: 32

Gnomad AFR AF: 0.183

Gnomad AMI AF: 0.00439

Gnomad AMR AF: 0.143

Gnomad ASJ AF: 0.0499

Gnomad EAS AF: 0.130

Gnomad SAS AF: 0.0920

Gnomad FIN AF: 0.0734

Gnomad MID AF: 0.0570

Gnomad NFE AF: 0.0347

Gnomad OTH AF: 0.0789

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

GnomAD4 genome AF: 0.0944 AC: 14346 AN: 151986 Hom.: 1026 Cov.: 32 AF XY: 0.0971 AC XY: 7214 AN XY: 74286

African (AFR) AF: 0.182 AC: 7556 AN: 41428

American (AMR) AF: 0.143 AC: 2179 AN: 15252

Ashkenazi Jewish (ASJ) AF: 0.0499 AC: 173 AN: 3464

East Asian (EAS) AF: 0.130 AC: 669 AN: 5158

South Asian (SAS) AF: 0.0917 AC: 440 AN: 4798

European-Finnish (FIN) AF: 0.0734 AC: 776 AN: 10574

Middle Eastern (MID) AF: 0.0612 AC: 18 AN: 294

European-Non Finnish (NFE) AF: 0.0347 AC: 2362 AN: 67994

Other (OTH) AF: 0.0800 AC: 169 AN: 2112

Alfa AF: 0.0563 Hom.: 1848

Bravo AF: 0.106

Asia WGS AF: 0.137 AC: 474 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	1.2
DANN	Benign	0.60
PhyloP100		0.079

Splicing

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

Other links and lift over

dbSNP: rs17109512; hg19: chr10-100127551;