4-132117054-A-G

Variant names:

• chr4-132117054-A-G
• rs1876054
• ENST00000420721.2:n.181+6797T>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000420721.2(ENSG00000251598):​n.181+6797T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.515 in 151,662 control chromosomes in the GnomAD database, including 20,123 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 0.52 (20123 hom., cov: 31)
• Consequence: ENSG00000251598 ENST00000420721.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.16
• Publications: 5 publications found

Genes affected

ENSG00000251598 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.539 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000420721.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000251598	ENST00000420721.2	TSL:4	n.181+6797T>C		intron	N/A
	ENSG00000251598	ENST00000652009.1		n.178-88573T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.515 AC: 78068 AN: 151544 Hom.: 20094 Cov.: 31

Gnomad AFR AF: 0.545

Gnomad AMI AF: 0.533

Gnomad AMR AF: 0.483

Gnomad ASJ AF: 0.604

Gnomad EAS AF: 0.518

Gnomad SAS AF: 0.501

Gnomad FIN AF: 0.490

Gnomad MID AF: 0.522

Gnomad NFE AF: 0.504

Gnomad OTH AF: 0.507

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

GnomAD4 genome AF: 0.515 AC: 78154 AN: 151662 Hom.: 20123 Cov.: 31 AF XY: 0.514 AC XY: 38105 AN XY: 74086

African (AFR) AF: 0.545 AC: 22555 AN: 41356

American (AMR) AF: 0.483 AC: 7345 AN: 15212

Ashkenazi Jewish (ASJ) AF: 0.604 AC: 2093 AN: 3464

East Asian (EAS) AF: 0.519 AC: 2681 AN: 5166

South Asian (SAS) AF: 0.501 AC: 2410 AN: 4808

European-Finnish (FIN) AF: 0.490 AC: 5149 AN: 10516

Middle Eastern (MID) AF: 0.510 AC: 149 AN: 292

European-Non Finnish (NFE) AF: 0.504 AC: 34213 AN: 67836

Other (OTH) AF: 0.511 AC: 1073 AN: 2100

Alfa AF: 0.514 Hom.: 6754

Bravo AF: 0.517

Asia WGS AF: 0.478 AC: 1658 AN: 3466

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.37
DANN	Benign	0.36
PhyloP100		-1.2

Splicing

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

Other links and lift over

dbSNP: rs1876054; hg19: chr4-133038209;