ENST00000725684.1:n.214+18058G>T

Variant names:

• chr8-40196086-C-A
• rs10958605
• ENST00000725684.1:n.214+18058G>T

Variant summary

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

The ENST00000725684.1(ENSG00000294749):​n.214+18058G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.36 in 151,974 control chromosomes in the GnomAD database, including 10,918 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 0.36 (10918 hom., cov: 32)
• Consequence: ENSG00000294749 ENST00000725684.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0110
• Publications: 10 publications found

Genes affected

ENSG00000294749 (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 (SAS) allele frequency at 95% confidence interval = 0.449 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
ENSG00000294749	ENST00000725684.1	n.214+18058G>T		intron_variant	Intron 1 of 3
ENSG00000294749	ENST00000725685.1	n.199+18058G>T		intron_variant	Intron 1 of 4
ENSG00000294749	ENST00000725686.1	n.175+18058G>T		intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes AF: 0.360 AC: 54675 AN: 151856 Hom.: 10917 Cov.: 32

Gnomad AFR AF: 0.169

Gnomad AMI AF: 0.436

Gnomad AMR AF: 0.434

Gnomad ASJ AF: 0.409

Gnomad EAS AF: 0.432

Gnomad SAS AF: 0.465

Gnomad FIN AF: 0.409

Gnomad MID AF: 0.449

Gnomad NFE AF: 0.435

Gnomad OTH AF: 0.392

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

GnomAD4 genome AF: 0.360 AC: 54689 AN: 151974 Hom.: 10918 Cov.: 32 AF XY: 0.361 AC XY: 26838 AN XY: 74266

African (AFR) AF: 0.168 AC: 6983 AN: 41474

American (AMR) AF: 0.434 AC: 6627 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.409 AC: 1417 AN: 3468

East Asian (EAS) AF: 0.431 AC: 2222 AN: 5152

South Asian (SAS) AF: 0.465 AC: 2244 AN: 4826

European-Finnish (FIN) AF: 0.409 AC: 4309 AN: 10536

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

European-Non Finnish (NFE) AF: 0.435 AC: 29530 AN: 67948

Other (OTH) AF: 0.394 AC: 830 AN: 2106

Alfa AF: 0.408 Hom.: 49117

Bravo AF: 0.356

Asia WGS AF: 0.441 AC: 1530 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	0.98
DANN	Benign	0.40
PhyloP100		0.011

Splicing

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

Other links and lift over

dbSNP: rs10958605; hg19: chr8-40053605;