4-117829193-T-C

Variant names:

• chr4-117829193-T-C
• rs1459528
• ENST00000767785.1:n.262-917A>G

Variant summary

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

The ENST00000767785.1(ENSG00000299982):​n.262-917A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.559 in 152,156 control chromosomes in the GnomAD database, including 26,549 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 0.56 (26549 hom., cov: 33)
• Consequence: ENSG00000299982 ENST00000767785.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.43
• Publications: 4 publications found

Genes affected

ENSG00000299982 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.846 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000767785.1. 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
	ENSG00000299982	ENST00000767785.1		n.262-917A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.559 AC: 84975 AN: 152038 Hom.: 26495 Cov.: 33

Gnomad AFR AF: 0.853

Gnomad AMI AF: 0.579

Gnomad AMR AF: 0.536

Gnomad ASJ AF: 0.497

Gnomad EAS AF: 0.632

Gnomad SAS AF: 0.421

Gnomad FIN AF: 0.416

Gnomad MID AF: 0.630

Gnomad NFE AF: 0.414

Gnomad OTH AF: 0.558

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

GnomAD4 genome AF: 0.559 AC: 85091 AN: 152156 Hom.: 26549 Cov.: 33 AF XY: 0.558 AC XY: 41475 AN XY: 74380

African (AFR) AF: 0.854 AC: 35476 AN: 41552

American (AMR) AF: 0.536 AC: 8195 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.497 AC: 1725 AN: 3470

East Asian (EAS) AF: 0.631 AC: 3254 AN: 5158

South Asian (SAS) AF: 0.422 AC: 2038 AN: 4826

European-Finnish (FIN) AF: 0.416 AC: 4398 AN: 10570

Middle Eastern (MID) AF: 0.633 AC: 186 AN: 294

European-Non Finnish (NFE) AF: 0.414 AC: 28118 AN: 67990

Other (OTH) AF: 0.558 AC: 1178 AN: 2112

Alfa AF: 0.424 Hom.: 2138

Bravo AF: 0.587

Asia WGS AF: 0.525 AC: 1824 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	1.0
DANN	Benign	0.49
PhyloP100		-1.4

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: rs1459528;

hg19: chr4-118750348;

COSMIC: COSV107199991;