5-85302499-G-T

Position:

• chr5-85302499-G-T

Variant summary

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

The XR_002956252.1(LOC101929321):​n.104+1587C>A 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 0.878 in 151,958 control chromosomes in the GnomAD database, including 58,893 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 0.88 (58893 hom., cov: 31)
• Consequence: LOC101929321 XR_002956252.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.67

Genes affected

LOC101929321 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.905 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC101929321	XR_002956252.1	n.104+1587C>A		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.878 AC: 133373 AN: 151842 Hom.: 58846 Cov.: 31

Gnomad AFR AF: 0.912

Gnomad AMI AF: 0.943

Gnomad AMR AF: 0.819

Gnomad ASJ AF: 0.934

Gnomad EAS AF: 0.637

Gnomad SAS AF: 0.831

Gnomad FIN AF: 0.853

Gnomad MID AF: 0.877

Gnomad NFE AF: 0.893

Gnomad OTH AF: 0.869

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

GnomAD4 genome AF: 0.878 AC: 133478 AN: 151958 Hom.: 58893 Cov.: 31 AF XY: 0.873 AC XY: 64840 AN XY: 74278

Gnomad4 AFR AF: 0.912

Gnomad4 AMR AF: 0.819

Gnomad4 ASJ AF: 0.934

Gnomad4 EAS AF: 0.637

Gnomad4 SAS AF: 0.830

Gnomad4 FIN AF: 0.853

Gnomad4 NFE AF: 0.893

Gnomad4 OTH AF: 0.869

Alfa AF: 0.887 Hom.: 43711

Bravo AF: 0.878

Asia WGS AF: 0.760 AC: 2637 AN: 3468

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.82
DANN	Benign	0.18

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4292478; hg19: chr5-84598317;