ENST00000662475.1:n.307+4607C>T

Variant names:

• chr4-87984751-G-A
• rs7655182
• ENST00000662475.1:n.307+4607C>T

Variant summary

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

The ENST00000662475.1(ENSG00000286618):​n.307+4607C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.412 in 151,932 control chromosomes in the GnomAD database, including 13,421 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 0.41 (13421 hom., cov: 32)
• Consequence: ENSG00000286618 ENST00000662475.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.575
• Publications: 6 publications found

Genes affected

ENSG00000286618 (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 (SAS) allele frequency at 95% confidence interval = 0.534 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000662475.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000286618	ENST00000662475.1		n.307+4607C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.412 AC: 62545 AN: 151814 Hom.: 13412 Cov.: 32

Gnomad AFR AF: 0.522

Gnomad AMI AF: 0.469

Gnomad AMR AF: 0.339

Gnomad ASJ AF: 0.366

Gnomad EAS AF: 0.458

Gnomad SAS AF: 0.552

Gnomad FIN AF: 0.424

Gnomad MID AF: 0.348

Gnomad NFE AF: 0.349

Gnomad OTH AF: 0.387

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

GnomAD4 genome AF: 0.412 AC: 62591 AN: 151932 Hom.: 13421 Cov.: 32 AF XY: 0.417 AC XY: 30917 AN XY: 74228

African (AFR) AF: 0.522 AC: 21610 AN: 41432

American (AMR) AF: 0.338 AC: 5166 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.366 AC: 1271 AN: 3472

East Asian (EAS) AF: 0.457 AC: 2352 AN: 5144

South Asian (SAS) AF: 0.551 AC: 2656 AN: 4816

European-Finnish (FIN) AF: 0.424 AC: 4483 AN: 10562

Middle Eastern (MID) AF: 0.350 AC: 103 AN: 294

European-Non Finnish (NFE) AF: 0.349 AC: 23702 AN: 67928

Other (OTH) AF: 0.389 AC: 821 AN: 2112

Alfa AF: 0.382 Hom.: 3445

Bravo AF: 0.414

Asia WGS AF: 0.514 AC: 1788 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.4
DANN	Benign	0.33
PhyloP100		-0.57

Splicing

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

Other links and lift over

dbSNP: rs7655182; hg19: chr4-88905903;