5-114498966-A-G

Position:

• chr5-114498966-A-G

Variant summary

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

The NR_130785.1(LOC101927078):​n.343-2788T>C 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 0.718 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: LOC101927078 NR_130785.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.707

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt
LOC101927078	NR_130785.1	n.343-2788T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000514115.6	n.332-2788T>C		intron_variant, non_coding_transcript_variant		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

Gnomad4 AFR AF: 0.606

Gnomad4 AMR AF: 0.800

Gnomad4 ASJ AF: 0.683

Gnomad4 EAS AF: 0.932

Gnomad4 SAS AF: 0.796

Gnomad4 FIN AF: 0.726

Gnomad4 NFE AF: 0.747

Gnomad4 OTH AF: 0.716

Alfa AF: 0.741 Hom.: 76751

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

Splicing

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

Publications

LitVar

Other links and lift over

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