rs17183114

Variant names:

• chr4-181301574-G-T
• rs17183114
• ENST00000807466.1:n.153-4414G>T

Variant summary

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

The ENST00000807466.1(ENSG00000304972):​n.153-4414G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.125 in 152,004 control chromosomes in the GnomAD database, including 1,306 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 0.13 (1306 hom., cov: 32)
• Consequence: ENSG00000304972 ENST00000807466.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.67
• Publications: 2 publications found

Genes affected

ENSG00000304972 (HGNC:):

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 (NFE) allele frequency at 95% confidence interval = 0.158 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000807466.1. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000304972	ENST00000807466.1		n.153-4414G>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.125 AC: 19015 AN: 151886 Hom.: 1307 Cov.: 32

Gnomad AFR AF: 0.0958

Gnomad AMI AF: 0.0504

Gnomad AMR AF: 0.102

Gnomad ASJ AF: 0.106

Gnomad EAS AF: 0.0390

Gnomad SAS AF: 0.0455

Gnomad FIN AF: 0.138

Gnomad MID AF: 0.105

Gnomad NFE AF: 0.160

Gnomad OTH AF: 0.132

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

GnomAD4 genome AF: 0.125 AC: 19018 AN: 152004 Hom.: 1306 Cov.: 32 AF XY: 0.122 AC XY: 9026 AN XY: 74286

African (AFR) AF: 0.0956 AC: 3967 AN: 41486

American (AMR) AF: 0.102 AC: 1555 AN: 15242

Ashkenazi Jewish (ASJ) AF: 0.106 AC: 369 AN: 3468

East Asian (EAS) AF: 0.0391 AC: 201 AN: 5144

South Asian (SAS) AF: 0.0455 AC: 219 AN: 4814

European-Finnish (FIN) AF: 0.138 AC: 1464 AN: 10588

Middle Eastern (MID) AF: 0.110 AC: 32 AN: 292

European-Non Finnish (NFE) AF: 0.160 AC: 10890 AN: 67956

Other (OTH) AF: 0.131 AC: 275 AN: 2102

Alfa AF: 0.148 Hom.: 6450

Bravo AF: 0.123

Asia WGS AF: 0.0460 AC: 160 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	0.10
DANN	Benign	0.54
PhyloP100		-1.7

Splicing

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

Other links and lift over

dbSNP: rs17183114; hg19: chr4-182222727;