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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC102723914	XR_427579.4	n.72-917A>G		intron_variant	Intron 1 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000299982	ENST00000767785.1	n.262-917A>G		intron_variant	Intron 3 of 3

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 v4.3

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

Other links and lift over

dbSNP: rs1459528; hg19: chr4-118750348; COSMIC: COSV107199991;