ENST00000662020.1:n.556-9451T>C

Variant names:

• chr4-127545545-A-G
• rs2090104
• ENST00000662020.1:n.556-9451T>C

Variant summary

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

The ENST00000662020.1(ENSG00000287021):​n.556-9451T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.417 in 152,006 control chromosomes in the GnomAD database, including 14,058 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 0.42 (14058 hom., cov: 32)
• Consequence: ENSG00000287021 ENST00000662020.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.119

Genes affected

ENSG00000287021 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.537 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
ENSG00000287021	ENST00000662020.1	n.556-9451T>C		intron_variant	Intron 5 of 5
ENSG00000287021	ENST00000668757.1	n.439-9451T>C		intron_variant	Intron 4 of 4

Frequencies

GnomAD3 genomes AF: 0.417 AC: 63300 AN: 151888 Hom.: 14021 Cov.: 32

Gnomad AFR AF: 0.543

Gnomad AMI AF: 0.192

Gnomad AMR AF: 0.496

Gnomad ASJ AF: 0.463

Gnomad EAS AF: 0.540

Gnomad SAS AF: 0.485

Gnomad FIN AF: 0.309

Gnomad MID AF: 0.513

Gnomad NFE AF: 0.325

Gnomad OTH AF: 0.436

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

GnomAD4 genome AF: 0.417 AC: 63398 AN: 152006 Hom.: 14058 Cov.: 32 AF XY: 0.419 AC XY: 31161 AN XY: 74298

Gnomad4 AFR AF: 0.543

Gnomad4 AMR AF: 0.496

Gnomad4 ASJ AF: 0.463

Gnomad4 EAS AF: 0.541

Gnomad4 SAS AF: 0.485

Gnomad4 FIN AF: 0.309

Gnomad4 NFE AF: 0.325

Gnomad4 OTH AF: 0.441

Alfa AF: 0.370 Hom.: 4265

Bravo AF: 0.435

Asia WGS AF: 0.525 AC: 1819 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	1.3
DANN	Benign	0.90

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2090104; hg19: chr4-128466700;