rs2416323

Variant names:

• chr5-113667696-C-T
• rs2416323
• ENST00000810862.1:n.390+14094C>T

Variant summary

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

The ENST00000810862.1(ENSG00000305424):​n.390+14094C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.114 in 152,074 control chromosomes in the GnomAD database, including 1,200 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 0.11 (1200 hom., cov: 33)
• Consequence: ENSG00000305424 ENST00000810862.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.210
• Publications: 1 publications found

Genes affected

ENSG00000305424 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.67).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.156 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000810862.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000305424	ENST00000810862.1		n.390+14094C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.114 AC: 17382 AN: 151956 Hom.: 1198 Cov.: 33

Gnomad AFR AF: 0.0411

Gnomad AMI AF: 0.167

Gnomad AMR AF: 0.140

Gnomad ASJ AF: 0.0823

Gnomad EAS AF: 0.0245

Gnomad SAS AF: 0.110

Gnomad FIN AF: 0.134

Gnomad MID AF: 0.0728

Gnomad NFE AF: 0.159

Gnomad OTH AF: 0.111

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

GnomAD4 genome AF: 0.114 AC: 17386 AN: 152074 Hom.: 1200 Cov.: 33 AF XY: 0.112 AC XY: 8359 AN XY: 74338

African (AFR) AF: 0.0410 AC: 1703 AN: 41510

American (AMR) AF: 0.140 AC: 2135 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.0823 AC: 285 AN: 3464

East Asian (EAS) AF: 0.0246 AC: 127 AN: 5164

South Asian (SAS) AF: 0.110 AC: 531 AN: 4812

European-Finnish (FIN) AF: 0.134 AC: 1420 AN: 10580

Middle Eastern (MID) AF: 0.0680 AC: 20 AN: 294

European-Non Finnish (NFE) AF: 0.159 AC: 10780 AN: 67960

Other (OTH) AF: 0.110 AC: 233 AN: 2114

Alfa AF: 0.129 Hom.: 167

Bravo AF: 0.109

Asia WGS AF: 0.0570 AC: 198 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.67
CADD	Benign	8.0
DANN	Benign	0.87
PhyloP100		0.21

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs2416323;

hg19: chr5-113003393;

COSMIC: COSV50462842;