chr4-116012923-C-T

Variant names:

• chr4-116012923-C-T
• rs7676999
• ENST00000508414.5:n.337-90788G>A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000508414.5(ENSG00000249259):​n.337-90788G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.163 in 151,830 control chromosomes in the GnomAD database, including 2,475 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 0.16 (2475 hom., cov: 32)
• Consequence: ENSG00000249259 ENST00000508414.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.818

Genes affected

ENSG00000249259 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.25 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000249259	ENST00000508414.5	n.337-90788G>A		intron_variant	Intron 2 of 2	3

Frequencies

GnomAD3 genomes AF: 0.163 AC: 24705 AN: 151710 Hom.: 2474 Cov.: 32

Gnomad AFR AF: 0.0551

Gnomad AMI AF: 0.218

Gnomad AMR AF: 0.148

Gnomad ASJ AF: 0.352

Gnomad EAS AF: 0.141

Gnomad SAS AF: 0.261

Gnomad FIN AF: 0.157

Gnomad MID AF: 0.287

Gnomad NFE AF: 0.216

Gnomad OTH AF: 0.183

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

GnomAD4 genome AF: 0.163 AC: 24711 AN: 151830 Hom.: 2475 Cov.: 32 AF XY: 0.162 AC XY: 12035 AN XY: 74162

Gnomad4 AFR AF: 0.0551

Gnomad4 AMR AF: 0.147

Gnomad4 ASJ AF: 0.352

Gnomad4 EAS AF: 0.141

Gnomad4 SAS AF: 0.262

Gnomad4 FIN AF: 0.157

Gnomad4 NFE AF: 0.216

Gnomad4 OTH AF: 0.181

Alfa AF: 0.188 Hom.: 1923

Bravo AF: 0.152

Asia WGS AF: 0.179 AC: 620 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	0.56
DANN	Benign	0.70

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs7676999; hg19: chr4-116934079;