rs4128340

Variant names:

• chr4-87986984-C-A
• rs4128340
• ENST00000662475.1:n.307+2374G>T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000662475.1(ENSG00000286618):​n.307+2374G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.343 in 151,924 control chromosomes in the GnomAD database, including 9,516 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 0.34 (9516 hom., cov: 32)
• Consequence: ENSG00000286618 ENST00000662475.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0290

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 (AFR) allele frequency at 95% confidence interval = 0.406 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+2374G>T		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.343 AC: 52128 AN: 151806 Hom.: 9511 Cov.: 32

Gnomad AFR AF: 0.412

Gnomad AMI AF: 0.377

Gnomad AMR AF: 0.271

Gnomad ASJ AF: 0.302

Gnomad EAS AF: 0.00212

Gnomad SAS AF: 0.225

Gnomad FIN AF: 0.380

Gnomad MID AF: 0.294

Gnomad NFE AF: 0.349

Gnomad OTH AF: 0.333

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

GnomAD4 genome AF: 0.343 AC: 52163 AN: 151924 Hom.: 9516 Cov.: 32 AF XY: 0.340 AC XY: 25276 AN XY: 74274

Gnomad4 AFR AF: 0.412

Gnomad4 AMR AF: 0.271

Gnomad4 ASJ AF: 0.302

Gnomad4 EAS AF: 0.00212

Gnomad4 SAS AF: 0.225

Gnomad4 FIN AF: 0.380

Gnomad4 NFE AF: 0.349

Gnomad4 OTH AF: 0.329

Alfa AF: 0.353 Hom.: 1181

Bravo AF: 0.334

Asia WGS AF: 0.131 AC: 454 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.0
DANN	Benign	0.14

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4128340; hg19: chr4-88908136;