5-132059045-C-T

Position:

• chr5-132059045-C-T

Variant summary

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

The XR_001742531.2(LOC105379174):​n.211+2426G>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 0.0718 in 152,268 control chromosomes in the GnomAD database, including 541 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 0.072 (541 hom., cov: 32)
• Consequence: LOC105379174 XR_001742531.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.678

Genes affected

LOC105379174 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.178 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105379174	XR_001742531.2	n.211+2426G>A		intron_variant, non_coding_transcript_variant
LOC105379174	XR_948784.3	n.398+2426G>A		intron_variant, non_coding_transcript_variant
LOC105379174	XR_948785.3	n.228+2426G>A		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.0718 AC: 10930 AN: 152150 Hom.: 542 Cov.: 32

Gnomad AFR AF: 0.0156

Gnomad AMI AF: 0.0779

Gnomad AMR AF: 0.0455

Gnomad ASJ AF: 0.108

Gnomad EAS AF: 0.188

Gnomad SAS AF: 0.0650

Gnomad FIN AF: 0.141

Gnomad MID AF: 0.0475

Gnomad NFE AF: 0.0914

Gnomad OTH AF: 0.0608

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

GnomAD4 genome AF: 0.0718 AC: 10927 AN: 152268 Hom.: 541 Cov.: 32 AF XY: 0.0738 AC XY: 5496 AN XY: 74440

Gnomad4 AFR AF: 0.0155

Gnomad4 AMR AF: 0.0455

Gnomad4 ASJ AF: 0.108

Gnomad4 EAS AF: 0.188

Gnomad4 SAS AF: 0.0651

Gnomad4 FIN AF: 0.141

Gnomad4 NFE AF: 0.0914

Gnomad4 OTH AF: 0.0611

Alfa AF: 0.0805 Hom.: 707

Bravo AF: 0.0624

Asia WGS AF: 0.0900 AC: 314 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	7.5
DANN	Benign	0.48

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2073506; hg19: chr5-131394738;