rs2914161

Positions:

• chr5-113687742-C-G

Variant summary

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

The XR_001742841.1(LOC107986441):​n.60-3317C>G 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 0.436 in 152,016 control chromosomes in the GnomAD database, including 17,547 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 0.44 (17547 hom., cov: 33)
• Consequence: LOC107986441 XR_001742841.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.831

Genes affected

LOC107986441 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.676 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC107986441	XR_001742841.1	n.60-3317C>G		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.436 AC: 66296 AN: 151898 Hom.: 17553 Cov.: 33

Gnomad AFR AF: 0.119

Gnomad AMI AF: 0.326

Gnomad AMR AF: 0.621

Gnomad ASJ AF: 0.578

Gnomad EAS AF: 0.695

Gnomad SAS AF: 0.662

Gnomad FIN AF: 0.547

Gnomad MID AF: 0.582

Gnomad NFE AF: 0.526

Gnomad OTH AF: 0.508

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

GnomAD4 genome AF: 0.436 AC: 66287 AN: 152016 Hom.: 17547 Cov.: 33 AF XY: 0.447 AC XY: 33234 AN XY: 74310

Gnomad4 AFR AF: 0.119

Gnomad4 AMR AF: 0.622

Gnomad4 ASJ AF: 0.578

Gnomad4 EAS AF: 0.695

Gnomad4 SAS AF: 0.662

Gnomad4 FIN AF: 0.547

Gnomad4 NFE AF: 0.526

Gnomad4 OTH AF: 0.505

Alfa AF: 0.457 Hom.: 2215

Bravo AF: 0.427

Asia WGS AF: 0.602 AC: 2092 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	1.6
DANN	Benign	0.54

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2914161; hg19: chr5-113023439;