4-187280196-T-G

Variant names:

• chr4-187280196-T-G
• rs4862792
• ENST00000795547.1:n.521-13874A>C

Variant summary

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

The ENST00000795547.1(ENSG00000250658):​n.521-13874A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.874 in 152,222 control chromosomes in the GnomAD database, including 58,171 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 0.87 (58171 hom., cov: 33)
• Consequence: ENSG00000250658 ENST00000795547.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.422
• Publications: 6 publications found

Genes affected

ENSG00000250658 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.884 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000795547.1. 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
	ENSG00000250658	ENST00000795547.1		n.521-13874A>C		intron	N/A
	ENSG00000250658	ENST00000795548.1		n.582-13874A>C		intron	N/A
	ENSG00000250658	ENST00000795549.1		n.580-13874A>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.874 AC: 132943 AN: 152104 Hom.: 58127 Cov.: 33

Gnomad AFR AF: 0.854

Gnomad AMI AF: 0.936

Gnomad AMR AF: 0.896

Gnomad ASJ AF: 0.869

Gnomad EAS AF: 0.849

Gnomad SAS AF: 0.888

Gnomad FIN AF: 0.885

Gnomad MID AF: 0.863

Gnomad NFE AF: 0.880

Gnomad OTH AF: 0.874

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

GnomAD4 genome AF: 0.874 AC: 133047 AN: 152222 Hom.: 58171 Cov.: 33 AF XY: 0.874 AC XY: 65025 AN XY: 74420

African (AFR) AF: 0.854 AC: 35443 AN: 41522

American (AMR) AF: 0.897 AC: 13723 AN: 15304

Ashkenazi Jewish (ASJ) AF: 0.869 AC: 3016 AN: 3472

East Asian (EAS) AF: 0.849 AC: 4376 AN: 5154

South Asian (SAS) AF: 0.889 AC: 4289 AN: 4826

European-Finnish (FIN) AF: 0.885 AC: 9384 AN: 10608

Middle Eastern (MID) AF: 0.877 AC: 256 AN: 292

European-Non Finnish (NFE) AF: 0.880 AC: 59861 AN: 68024

Other (OTH) AF: 0.875 AC: 1845 AN: 2108

Alfa AF: 0.878 Hom.: 127223

Bravo AF: 0.873

Asia WGS AF: 0.892 AC: 3103 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	1.5
DANN	Benign	0.42
PhyloP100		-0.42

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: rs4862792;

hg19: chr4-188201350;