ENST00000747096.1:n.267-7689C>T

Variant names:

• chr8-5907420-G-A
• rs2840445
• ENST00000747096.1:n.267-7689C>T

Variant summary

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

The ENST00000747096.1(ENSG00000297321):​n.267-7689C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.301 in 151,664 control chromosomes in the GnomAD database, including 7,084 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 0.30 (7084 hom., cov: 31)
• Consequence: ENSG00000297321 ENST00000747096.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0110
• Publications: 7 publications found

Genes affected

ENSG00000297321 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.52 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105377795	XR_001745765.1	n.308-7689C>T		intron_variant	Intron 3 of 5
LOC105377795	XR_001745766.1	n.406-7689C>T		intron_variant	Intron 3 of 5
LOC105377795	XR_001745767.1	n.216-7689C>T		intron_variant	Intron 2 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000297321	ENST00000747096.1	n.267-7689C>T		intron_variant	Intron 3 of 5
ENSG00000297321	ENST00000747097.1	n.169-7689C>T		intron_variant	Intron 2 of 4
ENSG00000297321	ENST00000747098.1	n.190-7689C>T		intron_variant	Intron 2 of 4

Frequencies

GnomAD3 genomes AF: 0.301 AC: 45541 AN: 151546 Hom.: 7067 Cov.: 31

Gnomad AFR AF: 0.323

Gnomad AMI AF: 0.345

Gnomad AMR AF: 0.310

Gnomad ASJ AF: 0.278

Gnomad EAS AF: 0.537

Gnomad SAS AF: 0.283

Gnomad FIN AF: 0.331

Gnomad MID AF: 0.225

Gnomad NFE AF: 0.265

Gnomad OTH AF: 0.283

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

GnomAD4 genome AF: 0.301 AC: 45594 AN: 151664 Hom.: 7084 Cov.: 31 AF XY: 0.306 AC XY: 22677 AN XY: 74100

African (AFR) AF: 0.324 AC: 13368 AN: 41320

American (AMR) AF: 0.309 AC: 4710 AN: 15228

Ashkenazi Jewish (ASJ) AF: 0.278 AC: 964 AN: 3464

East Asian (EAS) AF: 0.537 AC: 2743 AN: 5108

South Asian (SAS) AF: 0.283 AC: 1359 AN: 4802

European-Finnish (FIN) AF: 0.331 AC: 3478 AN: 10500

Middle Eastern (MID) AF: 0.214 AC: 63 AN: 294

European-Non Finnish (NFE) AF: 0.265 AC: 18008 AN: 67944

Other (OTH) AF: 0.280 AC: 587 AN: 2094

Alfa AF: 0.277 Hom.: 25665

Bravo AF: 0.303

Asia WGS AF: 0.343 AC: 1191 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	0.76
DANN	Benign	0.16
PhyloP100		-0.011

Splicing

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

Other links and lift over

dbSNP: rs2840445; hg19: chr8-5764942;