ENST00000740095.1:n.874+17968C>A

Variant names:

• chr13-63793037-G-T
• rs10507701
• ENST00000740095.1:n.874+17968C>A

Variant summary

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

The ENST00000740095.1(ENSG00000296525):​n.874+17968C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0464 in 152,120 control chromosomes in the GnomAD database, including 558 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 0.046 (558 hom., cov: 32)
• Consequence: ENSG00000296525 ENST00000740095.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.768
• Publications: 1 publications found

Genes affected

ENSG00000296525 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.153 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
ENSG00000296525	ENST00000740095.1	n.874+17968C>A		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.0463 AC: 7039 AN: 152004 Hom.: 555 Cov.: 32

Gnomad AFR AF: 0.156

Gnomad AMI AF: 0.00110

Gnomad AMR AF: 0.0152

Gnomad ASJ AF: 0.00807

Gnomad EAS AF: 0.000578

Gnomad SAS AF: 0.0162

Gnomad FIN AF: 0.000283

Gnomad MID AF: 0.0158

Gnomad NFE AF: 0.00250

Gnomad OTH AF: 0.0311

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

GnomAD4 genome AF: 0.0464 AC: 7051 AN: 152120 Hom.: 558 Cov.: 32 AF XY: 0.0438 AC XY: 3258 AN XY: 74364

African (AFR) AF: 0.156 AC: 6468 AN: 41420

American (AMR) AF: 0.0152 AC: 232 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.00807 AC: 28 AN: 3468

East Asian (EAS) AF: 0.000579 AC: 3 AN: 5178

South Asian (SAS) AF: 0.0160 AC: 77 AN: 4816

European-Finnish (FIN) AF: 0.000283 AC: 3 AN: 10612

Middle Eastern (MID) AF: 0.0136 AC: 4 AN: 294

European-Non Finnish (NFE) AF: 0.00250 AC: 170 AN: 68028

Other (OTH) AF: 0.0307 AC: 65 AN: 2114

Alfa AF: 0.0204 Hom.: 273

Bravo AF: 0.0514

Asia WGS AF: 0.0140 AC: 51 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.22
DANN	Benign	0.12
PhyloP100		-0.77

Splicing

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

Other links and lift over

dbSNP: rs10507701; hg19: chr13-64367170;