rs156500

Variant names:

• chr4-154756163-T-G
• rs156500
• ENST00000515071.1:n.417-1299A>C

Variant summary

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

The ENST00000515071.1(ENSG00000249041):​n.417-1299A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.145 in 151,972 control chromosomes in the GnomAD database, including 1,714 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 0.15 (1714 hom., cov: 31)
• Consequence: ENSG00000249041 ENST00000515071.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0650
• Publications: 7 publications found

Genes affected

ENSG00000249041 (HGNC:58901):

LOC105377500 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.74).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.209 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000515071.1. 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
	LOC105377500	NR_188451.1		n.417-1299A>C		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000249041	ENST00000515071.1	TSL:4	n.417-1299A>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.145 AC: 22082 AN: 151856 Hom.: 1706 Cov.: 31

Gnomad AFR AF: 0.177

Gnomad AMI AF: 0.0175

Gnomad AMR AF: 0.0884

Gnomad ASJ AF: 0.101

Gnomad EAS AF: 0.219

Gnomad SAS AF: 0.175

Gnomad FIN AF: 0.200

Gnomad MID AF: 0.140

Gnomad NFE AF: 0.127

Gnomad OTH AF: 0.140

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

GnomAD4 genome AF: 0.145 AC: 22104 AN: 151972 Hom.: 1714 Cov.: 31 AF XY: 0.148 AC XY: 10981 AN XY: 74274

African (AFR) AF: 0.177 AC: 7339 AN: 41440

American (AMR) AF: 0.0883 AC: 1347 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.101 AC: 352 AN: 3472

East Asian (EAS) AF: 0.219 AC: 1130 AN: 5156

South Asian (SAS) AF: 0.174 AC: 838 AN: 4806

European-Finnish (FIN) AF: 0.200 AC: 2112 AN: 10558

Middle Eastern (MID) AF: 0.143 AC: 42 AN: 294

European-Non Finnish (NFE) AF: 0.127 AC: 8637 AN: 67966

Other (OTH) AF: 0.138 AC: 291 AN: 2106

Alfa AF: 0.127 Hom.: 2078

Bravo AF: 0.139

Asia WGS AF: 0.170 AC: 592 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.74
CADD	Benign	7.8
DANN	Benign	0.92
PhyloP100		-0.065

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs156500;

hg19: chr4-155677315;