ENST00000654191.1:n.734-170409T>A

Variant names:

• chr10-64521033-T-A
• rs2394075
• ENST00000654191.1:n.734-170409T>A

Variant summary

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

The ENST00000654191.1(ENSG00000228566):​n.734-170409T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.527 in 151,822 control chromosomes in the GnomAD database, including 21,871 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 0.53 (21871 hom., cov: 30)
• Consequence: ENSG00000228566 ENST00000654191.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.130
• Publications: 2 publications found

Genes affected

ENSG00000228566 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.565 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC124902439	XR_007062160.1	n.713-170409T>A		intron_variant	Intron 4 of 5
LOC124902439	XR_007062161.1	n.715-170409T>A		intron_variant	Intron 4 of 5
LOC124902439	XR_007062165.1	n.270-170409T>A		intron_variant	Intron 2 of 3
LOC124902439	XR_007062166.1	n.433-170409T>A		intron_variant	Intron 2 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000228566	ENST00000654191.1	n.734-170409T>A		intron_variant	Intron 4 of 5
ENSG00000228566	ENST00000660795.1	n.580-170409T>A		intron_variant	Intron 5 of 6

Frequencies

GnomAD3 genomes AF: 0.528 AC: 80026 AN: 151702 Hom.: 21858 Cov.: 30

Gnomad AFR AF: 0.566

Gnomad AMI AF: 0.542

Gnomad AMR AF: 0.423

Gnomad ASJ AF: 0.464

Gnomad EAS AF: 0.0729

Gnomad SAS AF: 0.387

Gnomad FIN AF: 0.566

Gnomad MID AF: 0.459

Gnomad NFE AF: 0.570

Gnomad OTH AF: 0.506

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

GnomAD4 genome AF: 0.527 AC: 80067 AN: 151822 Hom.: 21871 Cov.: 30 AF XY: 0.520 AC XY: 38556 AN XY: 74180

African (AFR) AF: 0.566 AC: 23410 AN: 41382

American (AMR) AF: 0.423 AC: 6439 AN: 15226

Ashkenazi Jewish (ASJ) AF: 0.464 AC: 1611 AN: 3470

East Asian (EAS) AF: 0.0731 AC: 377 AN: 5156

South Asian (SAS) AF: 0.389 AC: 1868 AN: 4808

European-Finnish (FIN) AF: 0.566 AC: 5965 AN: 10540

Middle Eastern (MID) AF: 0.442 AC: 130 AN: 294

European-Non Finnish (NFE) AF: 0.570 AC: 38723 AN: 67930

Other (OTH) AF: 0.499 AC: 1050 AN: 2104

Alfa AF: 0.563 Hom.: 3031

Bravo AF: 0.516

Asia WGS AF: 0.243 AC: 847 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	2.3
DANN	Benign	0.79
PhyloP100		-0.13

Splicing

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

Other links and lift over

dbSNP: rs2394075; hg19: chr10-66280790;