4-116078416-T-C

Position:

• chr4-116078416-T-C

Variant summary

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

The ENST00000508414.5(ENSG00000293005):​n.336+118188A>G variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.71 in 152,062 control chromosomes in the GnomAD database, including 39,557 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 0.71 (39557 hom., cov: 31)
• Consequence: ENST00000508414.5 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.01

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.886 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000508414.5	n.336+118188A>G		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.710 AC: 107916 AN: 151944 Hom.: 39493 Cov.: 31

Gnomad AFR AF: 0.893

Gnomad AMI AF: 0.564

Gnomad AMR AF: 0.719

Gnomad ASJ AF: 0.701

Gnomad EAS AF: 0.596

Gnomad SAS AF: 0.779

Gnomad FIN AF: 0.635

Gnomad MID AF: 0.732

Gnomad NFE AF: 0.616

Gnomad OTH AF: 0.682

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

GnomAD4 genome AF: 0.710 AC: 108038 AN: 152062 Hom.: 39557 Cov.: 31 AF XY: 0.713 AC XY: 52975 AN XY: 74312

Gnomad4 AFR AF: 0.893

Gnomad4 AMR AF: 0.719

Gnomad4 ASJ AF: 0.701

Gnomad4 EAS AF: 0.597

Gnomad4 SAS AF: 0.780

Gnomad4 FIN AF: 0.635

Gnomad4 NFE AF: 0.616

Gnomad4 OTH AF: 0.681

Alfa AF: 0.637 Hom.: 52523

Bravo AF: 0.722

Asia WGS AF: 0.686 AC: 2389 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	2.6
DANN	Benign	0.33

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs814397; hg19: chr4-116999572;