ENST00000652889.2:n.123+17105A>G

Variant names:

• chr10-6970500-T-C
• rs1417032
• ENST00000652889.2:n.123+17105A>G

Variant summary

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

The ENST00000652889.2(ENSG00000287277):​n.123+17105A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.575 in 152,052 control chromosomes in the GnomAD database, including 25,501 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 0.58 (25501 hom., cov: 33)
• Consequence: ENSG00000287277 ENST00000652889.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.103
• Publications: 6 publications found

Genes affected

ENSG00000287277 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.619 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105376387	NR_188183.1	n.273-35092A>G		intron_variant	Intron 2 of 4
LOC105376387	NR_188184.1	n.74+17105A>G		intron_variant	Intron 1 of 4
LOC105376387	NR_188185.1	n.74+17105A>G		intron_variant	Intron 1 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000287277	ENST00000652889.2	n.123+17105A>G		intron_variant	Intron 1 of 3
ENSG00000287277	ENST00000654037.2	n.198+16036A>G		intron_variant	Intron 2 of 5
ENSG00000287277	ENST00000654694.1	n.80+17105A>G		intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes AF: 0.575 AC: 87397 AN: 151934 Hom.: 25496 Cov.: 33

Gnomad AFR AF: 0.554

Gnomad AMI AF: 0.538

Gnomad AMR AF: 0.497

Gnomad ASJ AF: 0.710

Gnomad EAS AF: 0.421

Gnomad SAS AF: 0.505

Gnomad FIN AF: 0.510

Gnomad MID AF: 0.810

Gnomad NFE AF: 0.624

Gnomad OTH AF: 0.610

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

GnomAD4 genome AF: 0.575 AC: 87436 AN: 152052 Hom.: 25501 Cov.: 33 AF XY: 0.568 AC XY: 42182 AN XY: 74326

African (AFR) AF: 0.554 AC: 22971 AN: 41466

American (AMR) AF: 0.496 AC: 7583 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.710 AC: 2463 AN: 3470

East Asian (EAS) AF: 0.421 AC: 2177 AN: 5170

South Asian (SAS) AF: 0.507 AC: 2442 AN: 4820

European-Finnish (FIN) AF: 0.510 AC: 5381 AN: 10556

Middle Eastern (MID) AF: 0.796 AC: 234 AN: 294

European-Non Finnish (NFE) AF: 0.624 AC: 42424 AN: 67976

Other (OTH) AF: 0.602 AC: 1270 AN: 2110

Alfa AF: 0.614 Hom.: 91192

Bravo AF: 0.573

Asia WGS AF: 0.404 AC: 1408 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	9.5
DANN	Benign	0.73
PhyloP100		0.10

Splicing

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

Other links and lift over

dbSNP: rs1417032; hg19: chr10-7012462;