4-127545545-A-G

Variant names:

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

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 4 publications found

Genes affected

ENSG00000287021 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000662020.1. 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
	ENSG00000287021	ENST00000662020.1		n.556-9451T>C		intron	N/A
	ENSG00000287021	ENST00000668757.1		n.439-9451T>C		intron	N/A
	ENSG00000287021	ENST00000828751.1		n.591-2969T>C		intron	N/A

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

African (AFR) AF: 0.543 AC: 22508 AN: 41460

American (AMR) AF: 0.496 AC: 7581 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.463 AC: 1606 AN: 3472

East Asian (EAS) AF: 0.541 AC: 2797 AN: 5174

South Asian (SAS) AF: 0.485 AC: 2336 AN: 4812

European-Finnish (FIN) AF: 0.309 AC: 3258 AN: 10548

Middle Eastern (MID) AF: 0.517 AC: 152 AN: 294

European-Non Finnish (NFE) AF: 0.325 AC: 22056 AN: 67960

Other (OTH) AF: 0.441 AC: 930 AN: 2108

Alfa AF: 0.371 Hom.: 20894

Bravo AF: 0.435

Asia WGS AF: 0.525 AC: 1819 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	1.3
DANN	Benign	0.90
PhyloP100		-0.12

Splicing

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

Other links and lift over

dbSNP: rs2090104; hg19: chr4-128466700;