rs2416323

Positions:

• chr5-113667696-C-T

Variant summary

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

The XR_001742841.1(LOC107986441):​n.60-23363C>T 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 0.114 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: LOC107986441 XR_001742841.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.210

Genes affected

LOC107986441 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC107986441	XR_001742841.1	n.60-23363C>T		intron_variant, non_coding_transcript_variant

Ensembl

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

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

Gnomad4 AFR AF: 0.0410

Gnomad4 AMR AF: 0.140

Gnomad4 ASJ AF: 0.0823

Gnomad4 EAS AF: 0.0246

Gnomad4 SAS AF: 0.110

Gnomad4 FIN AF: 0.134

Gnomad4 NFE AF: 0.159

Gnomad4 OTH AF: 0.110

Alfa AF: 0.131 Hom.: 166

Bravo AF: 0.109

Asia WGS AF: 0.0570 AC: 198 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2416323; hg19: chr5-113003393; COSMIC: COSV50462842;