5-114692144-G-C

Position:

• chr5-114692144-G-C

Variant summary

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

The variant allele was found at a frequency of 0.726 in 150,004 control chromosomes in the GnomAD database, including 40,095 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 0.73 (40095 hom., cov: 25)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0640

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.824 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.114692144G>C		intergenic_region
LOC101927078	NR_130785.1	n.80-23913C>G		intron_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.726 AC: 108798 AN: 149902 Hom.: 40060 Cov.: 25

Gnomad AFR AF: 0.832

Gnomad AMI AF: 0.823

Gnomad AMR AF: 0.652

Gnomad ASJ AF: 0.786

Gnomad EAS AF: 0.517

Gnomad SAS AF: 0.658

Gnomad FIN AF: 0.745

Gnomad MID AF: 0.861

Gnomad NFE AF: 0.690

Gnomad OTH AF: 0.750

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

GnomAD4 genome AF: 0.726 AC: 108875 AN: 150004 Hom.: 40095 Cov.: 25 AF XY: 0.724 AC XY: 52893 AN XY: 73062

Gnomad4 AFR AF: 0.832

Gnomad4 AMR AF: 0.652

Gnomad4 ASJ AF: 0.786

Gnomad4 EAS AF: 0.517

Gnomad4 SAS AF: 0.657

Gnomad4 FIN AF: 0.745

Gnomad4 NFE AF: 0.690

Gnomad4 OTH AF: 0.748

Alfa AF: 0.603 Hom.: 1718

Bravo AF: 0.726

Asia WGS AF: 0.563 AC: 1962 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.4
DANN	Benign	0.44

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs285912; hg19: chr5-114027841; COSMIC: COSV60184635;