5-158243581-T-G

Variant summary

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

The XR_001742535.2(LOC105377678):n.86+2113T>G 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 0.48 in 151,916 control chromosomes in the GnomAD database, including 18,333 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 0.48 (18333 hom., cov: 31)
• Consequence: LOC105377678 XR_001742535.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.16

Genes affected

LOC105377678 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.621 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105377678	XR_001742535.2	n.86+2113T>G		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.480 AC: 72864 AN: 151798 Hom.: 18290 Cov.: 31

Gnomad AFR AF: 0.627

Gnomad AMI AF: 0.344

Gnomad AMR AF: 0.456

Gnomad ASJ AF: 0.373

Gnomad EAS AF: 0.255

Gnomad SAS AF: 0.376

Gnomad FIN AF: 0.389

Gnomad MID AF: 0.459

Gnomad NFE AF: 0.443

Gnomad OTH AF: 0.450

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

GnomAD4 genome AF: 0.480 AC: 72962 AN: 151916 Hom.: 18333 Cov.: 31 AF XY: 0.477 AC XY: 35424 AN XY: 74242

Gnomad4 AFR AF: 0.628

Gnomad4 AMR AF: 0.456

Gnomad4 ASJ AF: 0.373

Gnomad4 EAS AF: 0.255

Gnomad4 SAS AF: 0.376

Gnomad4 FIN AF: 0.389

Gnomad4 NFE AF: 0.443

Gnomad4 OTH AF: 0.453

Alfa AF: 0.312 Hom.: 749

Bravo AF: 0.488

Asia WGS AF: 0.406 AC: 1413 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
Cadd	Benign	9.7
Dann	Benign	0.59

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1173466; hg19: chr5-157670589; COSMIC: COSV60220943;