chr4-177298634-C-T

Variant names:

• chr4-177298634-C-T
• rs1983132
• ENST00000656694.1:n.112+2413G>A

Variant summary

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

The ENST00000656694.1(ENSG00000287544):​n.112+2413G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.228 in 150,950 control chromosomes in the GnomAD database, including 5,132 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 0.23 (5132 hom., cov: 32)
• Consequence: ENSG00000287544 ENST00000656694.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.704
• Publications: 7 publications found

Genes affected

ENSG00000287544 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.414 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000656694.1. 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
	ENSG00000287544	ENST00000656694.1		n.112+2413G>A		intron	N/A
	ENSG00000287544	ENST00000662794.1		n.61+2413G>A		intron	N/A
	ENSG00000287544	ENST00000667713.1		n.207+2413G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.228 AC: 34389 AN: 150832 Hom.: 5098 Cov.: 32

Gnomad AFR AF: 0.419

Gnomad AMI AF: 0.174

Gnomad AMR AF: 0.228

Gnomad ASJ AF: 0.0974

Gnomad EAS AF: 0.166

Gnomad SAS AF: 0.289

Gnomad FIN AF: 0.167

Gnomad MID AF: 0.244

Gnomad NFE AF: 0.130

Gnomad OTH AF: 0.204

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

GnomAD4 genome AF: 0.228 AC: 34472 AN: 150950 Hom.: 5132 Cov.: 32 AF XY: 0.232 AC XY: 17061 AN XY: 73672

African (AFR) AF: 0.419 AC: 17288 AN: 41276

American (AMR) AF: 0.228 AC: 3454 AN: 15138

Ashkenazi Jewish (ASJ) AF: 0.0974 AC: 338 AN: 3470

East Asian (EAS) AF: 0.166 AC: 851 AN: 5114

South Asian (SAS) AF: 0.291 AC: 1383 AN: 4758

European-Finnish (FIN) AF: 0.167 AC: 1691 AN: 10114

Middle Eastern (MID) AF: 0.248 AC: 72 AN: 290

European-Non Finnish (NFE) AF: 0.130 AC: 8810 AN: 67784

Other (OTH) AF: 0.204 AC: 427 AN: 2096

Alfa AF: 0.160 Hom.: 2132

Bravo AF: 0.236

Asia WGS AF: 0.244 AC: 838 AN: 3418

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.011
DANN	Benign	0.20
PhyloP100		-0.70

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: rs1983132;

hg19: chr4-178219788;