rs7655182

Variant names:

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

Your query was ambiguous. Multiple possible variants found:

• chr4-87984751-G-A
• chr4-87984751-G-C

Variant summary

Our verdict is Benign. Variant got -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

Genes affected

ENSG00000286618 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

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
ENSG00000286618	ENST00000662475.1	n.307+4607C>T		intron_variant	Intron 2 of 2

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

Gnomad4 AFR AF: 0.522

Gnomad4 AMR AF: 0.338

Gnomad4 ASJ AF: 0.366

Gnomad4 EAS AF: 0.457

Gnomad4 SAS AF: 0.551

Gnomad4 FIN AF: 0.424

Gnomad4 NFE AF: 0.349

Gnomad4 OTH AF: 0.389

Alfa AF: 0.386 Hom.: 1962

Bravo AF: 0.414

Asia WGS AF: 0.514 AC: 1788 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	1.4
DANN	Benign	0.33

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7655182; hg19: chr4-88905903;