ENST00000650415.1:n.67-20147G>A

Variant names:

• chr7-25461637-G-A
• rs4719814
• ENST00000650415.1:n.67-20147G>A

Variant summary

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

The ENST00000650415.1(ENSG00000285960):​n.67-20147G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.642 in 151,972 control chromosomes in the GnomAD database, including 32,171 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 0.64 (32171 hom., cov: 32)
• Consequence: ENSG00000285960 ENST00000650415.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.137
• Publications: 2 publications found

Genes affected

ENSG00000285960 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.691 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
ENSG00000285960	ENST00000650415.1	n.67-20147G>A		intron_variant	Intron 1 of 2
ENSG00000309095	ENST00000838487.1	n.265+847G>A		intron_variant	Intron 1 of 2
ENSG00000309095	ENST00000838488.1	n.224+847G>A		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.642 AC: 97462 AN: 151854 Hom.: 32123 Cov.: 32

Gnomad AFR AF: 0.698

Gnomad AMI AF: 0.689

Gnomad AMR AF: 0.605

Gnomad ASJ AF: 0.575

Gnomad EAS AF: 0.180

Gnomad SAS AF: 0.485

Gnomad FIN AF: 0.693

Gnomad MID AF: 0.513

Gnomad NFE AF: 0.658

Gnomad OTH AF: 0.622

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

GnomAD4 genome AF: 0.642 AC: 97569 AN: 151972 Hom.: 32171 Cov.: 32 AF XY: 0.635 AC XY: 47197 AN XY: 74276

African (AFR) AF: 0.698 AC: 28916 AN: 41428

American (AMR) AF: 0.605 AC: 9238 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.575 AC: 1995 AN: 3468

East Asian (EAS) AF: 0.179 AC: 928 AN: 5174

South Asian (SAS) AF: 0.484 AC: 2327 AN: 4806

European-Finnish (FIN) AF: 0.693 AC: 7319 AN: 10556

Middle Eastern (MID) AF: 0.531 AC: 156 AN: 294

European-Non Finnish (NFE) AF: 0.658 AC: 44744 AN: 67960

Other (OTH) AF: 0.625 AC: 1318 AN: 2108

Alfa AF: 0.642 Hom.: 143419

Bravo AF: 0.635

Asia WGS AF: 0.399 AC: 1388 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	1.8
DANN	Benign	0.46
PhyloP100		-0.14

Splicing

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

Other links and lift over

dbSNP: rs4719814; hg19: chr7-25501256;