4-89859751-C-T

Variant names:

• chr4-89859751-C-T
• rs6532194
• ENST00000776860.1:n.209-18789G>A

Variant summary

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

The ENST00000776860.1(ENSG00000301182):​n.209-18789G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.234 in 148,956 control chromosomes in the GnomAD database, including 6,284 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 (6284 hom., cov: 30)
• Consequence: ENSG00000301182 ENST00000776860.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.190
• Publications: 19 publications found

Genes affected

ENSG00000301182 (HGNC:58852):

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 (EAS) allele frequency at 95% confidence interval = 0.534 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000776860.1. 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
	ENSG00000301182	ENST00000776860.1		n.209-18789G>A		intron	N/A
	ENSG00000301182	ENST00000776861.1		n.183-18789G>A		intron	N/A
	ENSG00000301182	ENST00000776862.1		n.81-4705G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.234 AC: 34826 AN: 148920 Hom.: 6274 Cov.: 30

Gnomad AFR AF: 0.456

Gnomad AMI AF: 0.0253

Gnomad AMR AF: 0.265

Gnomad ASJ AF: 0.170

Gnomad EAS AF: 0.552

Gnomad SAS AF: 0.268

Gnomad FIN AF: 0.130

Gnomad MID AF: 0.221

Gnomad NFE AF: 0.0874

Gnomad OTH AF: 0.242

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

GnomAD4 genome AF: 0.234 AC: 34840 AN: 148956 Hom.: 6284 Cov.: 30 AF XY: 0.237 AC XY: 17220 AN XY: 72524

African (AFR) AF: 0.456 AC: 18540 AN: 40622

American (AMR) AF: 0.265 AC: 3937 AN: 14838

Ashkenazi Jewish (ASJ) AF: 0.170 AC: 586 AN: 3452

East Asian (EAS) AF: 0.551 AC: 2804 AN: 5090

South Asian (SAS) AF: 0.266 AC: 1263 AN: 4744

European-Finnish (FIN) AF: 0.130 AC: 1229 AN: 9478

Middle Eastern (MID) AF: 0.216 AC: 61 AN: 282

European-Non Finnish (NFE) AF: 0.0874 AC: 5896 AN: 67476

Other (OTH) AF: 0.243 AC: 501 AN: 2064

Alfa AF: 0.132 Hom.: 8126

Bravo AF: 0.258

Asia WGS AF: 0.415 AC: 1441 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	1.4
DANN	Benign	0.22
PhyloP100		0.19

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: rs6532194;

hg19: chr4-90780902;