rs814397

Variant names:

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

Your query was ambiguous. Multiple possible variants found:

• chr4-116078416-T-C
• chr4-116078416-T-G

Variant summary

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

The ENST00000508414.5(ENSG00000249259):​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: ENSG00000249259 ENST00000508414.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.01

Genes affected

ENSG00000249259 (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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000249259	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

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;