ENST00000650415.1:n.66+4652T>C

Variant names:

• chr7-25436697-T-C
• rs1476697
• ENST00000650415.1:n.66+4652T>C

Variant summary

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

The ENST00000650415.1(ENSG00000285960):​n.66+4652T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.312 in 152,166 control chromosomes in the GnomAD database, including 8,683 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 0.31 (8683 hom., cov: 33)
• Consequence: ENSG00000285960 ENST00000650415.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.297
• Publications: 5 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=-0.78).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.792 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000650415.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000285960	ENST00000650415.1		n.66+4652T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.312 AC: 47432 AN: 152048 Hom.: 8697 Cov.: 33

Gnomad AFR AF: 0.170

Gnomad AMI AF: 0.285

Gnomad AMR AF: 0.375

Gnomad ASJ AF: 0.459

Gnomad EAS AF: 0.813

Gnomad SAS AF: 0.497

Gnomad FIN AF: 0.307

Gnomad MID AF: 0.560

Gnomad NFE AF: 0.324

Gnomad OTH AF: 0.348

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

GnomAD4 genome AF: 0.312 AC: 47429 AN: 152166 Hom.: 8683 Cov.: 33 AF XY: 0.319 AC XY: 23764 AN XY: 74392

African (AFR) AF: 0.170 AC: 7063 AN: 41538

American (AMR) AF: 0.375 AC: 5725 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.459 AC: 1592 AN: 3472

East Asian (EAS) AF: 0.812 AC: 4210 AN: 5182

South Asian (SAS) AF: 0.497 AC: 2398 AN: 4828

European-Finnish (FIN) AF: 0.307 AC: 3248 AN: 10586

Middle Eastern (MID) AF: 0.537 AC: 158 AN: 294

European-Non Finnish (NFE) AF: 0.324 AC: 22050 AN: 67986

Other (OTH) AF: 0.344 AC: 726 AN: 2110

Alfa AF: 0.332 Hom.: 36805

Bravo AF: 0.313

Asia WGS AF: 0.589 AC: 2043 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
CADD	Benign	1.9
DANN	Benign	0.85
PhyloP100		0.30

Splicing

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

Other links and lift over

dbSNP: rs1476697; hg19: chr7-25476316;