ENST00000661640.1:n.335+4023C>A

Variant names:

• chr6-457748-C-A
• rs4959270
• ENST00000661640.1:n.335+4023C>A

Variant summary

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

The ENST00000661640.1(ENSG00000286364):​n.335+4023C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.41 in 152,016 control chromosomes in the GnomAD database, including 13,643 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 (13643 hom., cov: 32)
• Consequence: ENSG00000286364 ENST00000661640.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.210

Genes affected

ENSG00000286364 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.484 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
ENSG00000286364	ENST00000661640.1	n.335+4023C>A		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.410 AC: 62294 AN: 151896 Hom.: 13632 Cov.: 32

Gnomad AFR AF: 0.259

Gnomad AMI AF: 0.277

Gnomad AMR AF: 0.485

Gnomad ASJ AF: 0.468

Gnomad EAS AF: 0.337

Gnomad SAS AF: 0.287

Gnomad FIN AF: 0.469

Gnomad MID AF: 0.411

Gnomad NFE AF: 0.488

Gnomad OTH AF: 0.437

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

GnomAD4 genome AF: 0.410 AC: 62336 AN: 152016 Hom.: 13643 Cov.: 32 AF XY: 0.407 AC XY: 30243 AN XY: 74324

Gnomad4 AFR AF: 0.259

Gnomad4 AMR AF: 0.485

Gnomad4 ASJ AF: 0.468

Gnomad4 EAS AF: 0.338

Gnomad4 SAS AF: 0.288

Gnomad4 FIN AF: 0.469

Gnomad4 NFE AF: 0.488

Gnomad4 OTH AF: 0.443

Alfa AF: 0.464 Hom.: 22579

Bravo AF: 0.406

Asia WGS AF: 0.346 AC: 1203 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	1.3
DANN	Benign	0.32

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4959270; hg19: chr6-457748;