4-174537138-C-A

Variant names:

• chr4-174537138-C-A
• rs2251316
• ENST00000515178.1:n.1145-548G>T

Variant summary

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

The ENST00000515178.1(ENSG00000293043):​n.1145-548G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.323 in 151,878 control chromosomes in the GnomAD database, including 8,170 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 0.32 (8170 hom., cov: 32)
• Consequence: ENSG00000293043 ENST00000515178.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.396
• Publications: 4 publications found

Genes affected

ENSG00000293043 (HGNC:):

ENSG00000251584 (HGNC:58913):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.455 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000515178.1. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000293043	ENST00000515178.1	TSL:1	n.1145-548G>T		intron	N/A
	ENSG00000251584	ENST00000507483.1	TSL:3	n.242+257C>A		intron	N/A
	ENSG00000251584	ENST00000664316.1		n.478-994C>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.323 AC: 48961 AN: 151760 Hom.: 8160 Cov.: 32

Gnomad AFR AF: 0.379

Gnomad AMI AF: 0.245

Gnomad AMR AF: 0.296

Gnomad ASJ AF: 0.263

Gnomad EAS AF: 0.470

Gnomad SAS AF: 0.159

Gnomad FIN AF: 0.284

Gnomad MID AF: 0.188

Gnomad NFE AF: 0.307

Gnomad OTH AF: 0.292

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

GnomAD4 genome AF: 0.323 AC: 48996 AN: 151878 Hom.: 8170 Cov.: 32 AF XY: 0.317 AC XY: 23539 AN XY: 74210

African (AFR) AF: 0.379 AC: 15679 AN: 41418

American (AMR) AF: 0.296 AC: 4513 AN: 15234

Ashkenazi Jewish (ASJ) AF: 0.263 AC: 913 AN: 3470

East Asian (EAS) AF: 0.470 AC: 2424 AN: 5154

South Asian (SAS) AF: 0.159 AC: 766 AN: 4814

European-Finnish (FIN) AF: 0.284 AC: 2990 AN: 10538

Middle Eastern (MID) AF: 0.184 AC: 54 AN: 294

European-Non Finnish (NFE) AF: 0.307 AC: 20827 AN: 67942

Other (OTH) AF: 0.288 AC: 607 AN: 2104

Alfa AF: 0.297 Hom.: 11871

Bravo AF: 0.328

Asia WGS AF: 0.282 AC: 980 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.32
DANN	Benign	0.31
PhyloP100		-0.40

Splicing

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

Other links and lift over

dbSNP: rs2251316; hg19: chr4-175458289;