5-96246669-C-T

Position:

• chr5-96246669-C-T

Variant summary

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

The NR_130776.1(LOC101929710):​n.37-62055C>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 0.126 in 152,122 control chromosomes in the GnomAD database, including 1,571 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 0.13 (1571 hom., cov: 31)
• Consequence: LOC101929710 NR_130776.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.351

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.209 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC101929710	NR_130776.1	n.37-62055C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000502645.2	n.37-62055C>T		intron_variant, non_coding_transcript_variant		5
	ENST00000511775.1	n.36-71804C>T		intron_variant, non_coding_transcript_variant		4

Frequencies

GnomAD3 genomes AF: 0.126 AC: 19109 AN: 152002 Hom.: 1565 Cov.: 31

Gnomad AFR AF: 0.204

Gnomad AMI AF: 0.114

Gnomad AMR AF: 0.145

Gnomad ASJ AF: 0.0660

Gnomad EAS AF: 0.220

Gnomad SAS AF: 0.156

Gnomad FIN AF: 0.0771

Gnomad MID AF: 0.0791

Gnomad NFE AF: 0.0763

Gnomad OTH AF: 0.107

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

GnomAD4 genome AF: 0.126 AC: 19141 AN: 152122 Hom.: 1571 Cov.: 31 AF XY: 0.125 AC XY: 9301 AN XY: 74364

Gnomad4 AFR AF: 0.204

Gnomad4 AMR AF: 0.145

Gnomad4 ASJ AF: 0.0660

Gnomad4 EAS AF: 0.219

Gnomad4 SAS AF: 0.156

Gnomad4 FIN AF: 0.0771

Gnomad4 NFE AF: 0.0763

Gnomad4 OTH AF: 0.106

Alfa AF: 0.0983 Hom.: 132

Bravo AF: 0.134

Asia WGS AF: 0.209 AC: 728 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	2.5
DANN	Benign	0.65

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4077817; hg19: chr5-95582373;