5-114498966-A-G

Variant names:

• chr5-114498966-A-G
• rs3891371
• ENST00000514115.6:n.332-2788T>C

Variant summary

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

The ENST00000514115.6(ENSG00000246316):​n.332-2788T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.718 in 152,066 control chromosomes in the GnomAD database, including 39,604 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 0.72 (39604 hom., cov: 32)
• Consequence: ENSG00000246316 ENST00000514115.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.707
• Publications: 5 publications found

Genes affected

ENSG00000246316 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.909 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC101927078	NR_130785.1	n.343-2788T>C		intron_variant	Intron 3 of 12

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000246316	ENST00000514115.6	n.332-2788T>C		intron_variant	Intron 3 of 6	3

Frequencies

GnomAD3 genomes AF: 0.718 AC: 109082 AN: 151948 Hom.: 39584 Cov.: 32

Gnomad AFR AF: 0.606

Gnomad AMI AF: 0.764

Gnomad AMR AF: 0.799

Gnomad ASJ AF: 0.683

Gnomad EAS AF: 0.931

Gnomad SAS AF: 0.797

Gnomad FIN AF: 0.726

Gnomad MID AF: 0.620

Gnomad NFE AF: 0.747

Gnomad OTH AF: 0.716

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

GnomAD4 genome AF: 0.718 AC: 109148 AN: 152066 Hom.: 39604 Cov.: 32 AF XY: 0.721 AC XY: 53587 AN XY: 74320

African (AFR) AF: 0.606 AC: 25109 AN: 41464

American (AMR) AF: 0.800 AC: 12222 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.683 AC: 2370 AN: 3472

East Asian (EAS) AF: 0.932 AC: 4788 AN: 5140

South Asian (SAS) AF: 0.796 AC: 3838 AN: 4824

European-Finnish (FIN) AF: 0.726 AC: 7674 AN: 10576

Middle Eastern (MID) AF: 0.619 AC: 182 AN: 294

European-Non Finnish (NFE) AF: 0.747 AC: 50755 AN: 67986

Other (OTH) AF: 0.716 AC: 1513 AN: 2112

Alfa AF: 0.740 Hom.: 167146

Bravo AF: 0.719

Asia WGS AF: 0.807 AC: 2802 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	7.6
DANN	Benign	0.36
PhyloP100		0.71

Splicing

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

Other links and lift over

dbSNP: rs3891371; hg19: chr5-113834663; COSMIC: COSV53286096;