chr4-154757193-C-T

Variant names:

• chr4-154757193-C-T
• rs156501
• ENST00000515071.1:n.417-2329G>A

Variant summary

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

The ENST00000515071.1(ENSG00000249041):​n.417-2329G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.249 in 152,096 control chromosomes in the GnomAD database, including 4,964 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 0.25 (4964 hom., cov: 32)
• Consequence: ENSG00000249041 ENST00000515071.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.07
• Publications: 7 publications found

Genes affected

ENSG00000249041 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.342 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105377500	NR_188451.1	n.417-2329G>A		intron_variant	Intron 3 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000249041	ENST00000515071.1	n.417-2329G>A		intron_variant	Intron 3 of 3	4

Frequencies

GnomAD3 genomes AF: 0.249 AC: 37826 AN: 151978 Hom.: 4951 Cov.: 32

Gnomad AFR AF: 0.253

Gnomad AMI AF: 0.0789

Gnomad AMR AF: 0.349

Gnomad ASJ AF: 0.185

Gnomad EAS AF: 0.242

Gnomad SAS AF: 0.355

Gnomad FIN AF: 0.323

Gnomad MID AF: 0.287

Gnomad NFE AF: 0.211

Gnomad OTH AF: 0.235

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

GnomAD4 genome AF: 0.249 AC: 37871 AN: 152096 Hom.: 4964 Cov.: 32 AF XY: 0.257 AC XY: 19102 AN XY: 74322

African (AFR) AF: 0.254 AC: 10522 AN: 41492

American (AMR) AF: 0.350 AC: 5345 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.185 AC: 641 AN: 3470

East Asian (EAS) AF: 0.241 AC: 1248 AN: 5174

South Asian (SAS) AF: 0.354 AC: 1707 AN: 4820

European-Finnish (FIN) AF: 0.323 AC: 3416 AN: 10566

Middle Eastern (MID) AF: 0.284 AC: 83 AN: 292

European-Non Finnish (NFE) AF: 0.211 AC: 14340 AN: 67968

Other (OTH) AF: 0.235 AC: 497 AN: 2112

Alfa AF: 0.218 Hom.: 17000

Bravo AF: 0.248

Asia WGS AF: 0.298 AC: 1039 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.17
DANN	Benign	0.19
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs156501; hg19: chr4-155678345;