chr4-116078416-T-C

Variant names:

• chr4-116078416-T-C
• rs814397
• ENST00000508414.5:n.336+118188A>G

Variant summary

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

The ENST00000508414.5(ENSG00000293005):​n.336+118188A>G variant causes a intron 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: ENSG00000293005 ENST00000508414.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.01
• Publications: 4 publications found

Genes affected

ENSG00000293005 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000293005	ENST00000508414.5	n.336+118188A>G		intron_variant	Intron 2 of 2	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

African (AFR) AF: 0.893 AC: 37080 AN: 41508

American (AMR) AF: 0.719 AC: 10996 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.701 AC: 2432 AN: 3468

East Asian (EAS) AF: 0.597 AC: 3071 AN: 5148

South Asian (SAS) AF: 0.780 AC: 3748 AN: 4808

European-Finnish (FIN) AF: 0.635 AC: 6706 AN: 10562

Middle Eastern (MID) AF: 0.740 AC: 216 AN: 292

European-Non Finnish (NFE) AF: 0.616 AC: 41839 AN: 67964

Other (OTH) AF: 0.681 AC: 1436 AN: 2110

Alfa AF: 0.648 Hom.: 123466

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
PhyloP100		-1.0

Splicing

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

Other links and lift over

dbSNP: rs814397; hg19: chr4-116999572;