chr4-27743096-C-T

Variant names:

• chr4-27743096-C-T
• rs4692256
• ENST00000849360.1:n.139-2325C>T

Variant summary

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

The ENST00000849360.1(ENSG00000310375):​n.139-2325C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.615 in 151,486 control chromosomes in the GnomAD database, including 29,177 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 0.61 (29177 hom., cov: 31)
• Consequence: ENSG00000310375 ENST00000849360.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.143
• Publications: 11 publications found

Genes affected

ENSG00000310375 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.718 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000849360.1. 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
	ENSG00000310375	ENST00000849360.1		n.139-2325C>T		intron	N/A
	ENSG00000310375	ENST00000849361.1		n.332-2325C>T		intron	N/A
	ENSG00000310375	ENST00000849362.1		n.139-2325C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.614 AC: 93014 AN: 151368 Hom.: 29144 Cov.: 31

Gnomad AFR AF: 0.725

Gnomad AMI AF: 0.649

Gnomad AMR AF: 0.602

Gnomad ASJ AF: 0.576

Gnomad EAS AF: 0.724

Gnomad SAS AF: 0.549

Gnomad FIN AF: 0.615

Gnomad MID AF: 0.522

Gnomad NFE AF: 0.549

Gnomad OTH AF: 0.591

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

GnomAD4 genome AF: 0.615 AC: 93112 AN: 151486 Hom.: 29177 Cov.: 31 AF XY: 0.615 AC XY: 45493 AN XY: 74022

African (AFR) AF: 0.725 AC: 29986 AN: 41354

American (AMR) AF: 0.603 AC: 9148 AN: 15178

Ashkenazi Jewish (ASJ) AF: 0.576 AC: 1990 AN: 3456

East Asian (EAS) AF: 0.724 AC: 3701 AN: 5110

South Asian (SAS) AF: 0.548 AC: 2648 AN: 4830

European-Finnish (FIN) AF: 0.615 AC: 6494 AN: 10552

Middle Eastern (MID) AF: 0.517 AC: 152 AN: 294

European-Non Finnish (NFE) AF: 0.549 AC: 37152 AN: 67696

Other (OTH) AF: 0.594 AC: 1252 AN: 2108

Alfa AF: 0.566 Hom.: 73739

Bravo AF: 0.618

Asia WGS AF: 0.648 AC: 2252 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.2
DANN	Benign	0.20
PhyloP100		-0.14

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: rs4692256;

hg19: chr4-27744718;