4-116067741-G-A

Variant names:

• chr4-116067741-G-A
• rs1103021
• ENST00000508414.5:n.336+128863C>T

Variant summary

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

The ENST00000508414.5(ENSG00000293005):​n.336+128863C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.7 in 151,894 control chromosomes in the GnomAD database, including 38,214 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 0.70 (38214 hom., cov: 31)
• Consequence: ENSG00000293005 ENST00000508414.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.89
• Publications: 2 publications found

Genes affected

ENSG00000293005 (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 = 0.855 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000508414.5. 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
	ENSG00000293005	ENST00000508414.5	TSL:3	n.336+128863C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.700 AC: 106234 AN: 151776 Hom.: 38152 Cov.: 31

Gnomad AFR AF: 0.862

Gnomad AMI AF: 0.563

Gnomad AMR AF: 0.717

Gnomad ASJ AF: 0.694

Gnomad EAS AF: 0.595

Gnomad SAS AF: 0.783

Gnomad FIN AF: 0.604

Gnomad MID AF: 0.731

Gnomad NFE AF: 0.617

Gnomad OTH AF: 0.683

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

GnomAD4 genome AF: 0.700 AC: 106354 AN: 151894 Hom.: 38214 Cov.: 31 AF XY: 0.701 AC XY: 52030 AN XY: 74232

African (AFR) AF: 0.863 AC: 35760 AN: 41454

American (AMR) AF: 0.718 AC: 10958 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.694 AC: 2408 AN: 3468

East Asian (EAS) AF: 0.596 AC: 3061 AN: 5136

South Asian (SAS) AF: 0.783 AC: 3778 AN: 4824

European-Finnish (FIN) AF: 0.604 AC: 6333 AN: 10488

Middle Eastern (MID) AF: 0.738 AC: 214 AN: 290

European-Non Finnish (NFE) AF: 0.617 AC: 41894 AN: 67944

Other (OTH) AF: 0.681 AC: 1436 AN: 2108

Alfa AF: 0.662 Hom.: 4200

Bravo AF: 0.713

Asia WGS AF: 0.684 AC: 2377 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.14
DANN	Benign	0.63
PhyloP100		-1.9

Splicing

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

Other links and lift over

dbSNP: rs1103021; hg19: chr4-116988897;