4-116238655-C-T

Variant names:

• chr4-116238655-C-T
• rs1965299
• ENST00000508414.5:n.203-41918G>A

Variant summary

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

The ENST00000508414.5(ENSG00000249259):​n.203-41918G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.798 in 151,942 control chromosomes in the GnomAD database, including 48,624 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 0.80 (48624 hom., cov: 31)
• Consequence: ENSG00000249259 ENST00000508414.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.674

Genes affected

ENSG00000249259 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.897 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.203-41918G>A		intron_variant	Intron 1 of 2	3
ENSG00000249259	ENST00000509983.1	n.200-41918G>A		intron_variant	Intron 1 of 2	3

Frequencies

GnomAD3 genomes AF: 0.798 AC: 121132 AN: 151824 Hom.: 48603 Cov.: 31

Gnomad AFR AF: 0.718

Gnomad AMI AF: 0.916

Gnomad AMR AF: 0.808

Gnomad ASJ AF: 0.735

Gnomad EAS AF: 0.918

Gnomad SAS AF: 0.787

Gnomad FIN AF: 0.863

Gnomad MID AF: 0.677

Gnomad NFE AF: 0.829

Gnomad OTH AF: 0.768

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

GnomAD4 genome AF: 0.798 AC: 121206 AN: 151942 Hom.: 48624 Cov.: 31 AF XY: 0.798 AC XY: 59312 AN XY: 74284

Gnomad4 AFR AF: 0.717

Gnomad4 AMR AF: 0.808

Gnomad4 ASJ AF: 0.735

Gnomad4 EAS AF: 0.918

Gnomad4 SAS AF: 0.787

Gnomad4 FIN AF: 0.863

Gnomad4 NFE AF: 0.829

Gnomad4 OTH AF: 0.767

Alfa AF: 0.819 Hom.: 103287

Bravo AF: 0.791

Asia WGS AF: 0.831 AC: 2870 AN: 3454

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.1
DANN	Benign	0.36

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1965299; hg19: chr4-117159811;