chr5-145457527-C-T

Position:

• chr5-145457527-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The XR_007058983.1(LOC105378211):​n.60-21474C>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 0.0106 in 152,204 control chromosomes in the GnomAD database, including 15 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 0.011 (15 hom., cov: 32)
• Consequence: LOC105378211 XR_007058983.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.10

Genes affected

LOC105378211 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BS1: Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.0106 (1610/152204) while in subpopulation AFR AF= 0.0232 (964/41550). AF 95% confidence interval is 0.022. There are 15 homozygotes in gnomad4. There are 767 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
• BS2: High Homozygotes in GnomAd4 at 15 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105378211	XR_007058983.1	n.60-21474C>T		intron_variant, non_coding_transcript_variant
LOC105378211	XR_001742911.2	n.60-21474C>T		intron_variant, non_coding_transcript_variant
PRELID2	XR_007058586.1	n.751+15673G>A		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.0105 AC: 1593 AN: 152086 Hom.: 12 Cov.: 32

Gnomad AFR AF: 0.0229

Gnomad AMI AF: 0.0329

Gnomad AMR AF: 0.00623

Gnomad ASJ AF: 0.00691

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.000829

Gnomad FIN AF: 0.00170

Gnomad MID AF: 0.00318

Gnomad NFE AF: 0.00665

Gnomad OTH AF: 0.0105

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

GnomAD4 genome AF: 0.0106 AC: 1610 AN: 152204 Hom.: 15 Cov.: 32 AF XY: 0.0103 AC XY: 767 AN XY: 74398

Gnomad4 AFR AF: 0.0232

Gnomad4 AMR AF: 0.00622

Gnomad4 ASJ AF: 0.00691

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.000829

Gnomad4 FIN AF: 0.00170

Gnomad4 NFE AF: 0.00665

Gnomad4 OTH AF: 0.0104

Alfa AF: 0.00844 Hom.: 0

Bravo AF: 0.0119

Asia WGS AF: 0.00231 AC: 8 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.090
DANN	Benign	0.50

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3909378; hg19: chr5-144837090;