rs1146904

chr13-76521501-G-A

Variant summary

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

The XR_001749919.1(LOC105370263):n.158-4166G>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 0.537 in 151,960 control chromosomes in the GnomAD database, including 22,196 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 0.54 (22196 hom., cov: 32)
• Consequence: LOC105370263 XR_001749919.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.561

Genes affected

LOC105370263 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.648 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105370263	XR_001749919.1	n.158-4166G>A		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.537 AC: 81551 AN: 151840 Hom.: 22169 Cov.: 32

Gnomad AFR AF: 0.548

Gnomad AMI AF: 0.571

Gnomad AMR AF: 0.658

Gnomad ASJ AF: 0.539

Gnomad EAS AF: 0.476

Gnomad SAS AF: 0.593

Gnomad FIN AF: 0.444

Gnomad MID AF: 0.652

Gnomad NFE AF: 0.516

Gnomad OTH AF: 0.573

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

GnomAD4 genome AF: 0.537 AC: 81617 AN: 151960 Hom.: 22196 Cov.: 32 AF XY: 0.538 AC XY: 39962 AN XY: 74236

Gnomad4 AFR AF: 0.548

Gnomad4 AMR AF: 0.659

Gnomad4 ASJ AF: 0.539

Gnomad4 EAS AF: 0.476

Gnomad4 SAS AF: 0.594

Gnomad4 FIN AF: 0.444

Gnomad4 NFE AF: 0.516

Gnomad4 OTH AF: 0.569

Alfa AF: 0.525 Hom.: 9915

Bravo AF: 0.554

Asia WGS AF: 0.536 AC: 1867 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
Cadd	Benign	0.10
Dann	Benign	0.76

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1146904; hg19: chr13-77095636;