18-49708823-T-C

Variant summary

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

The XR_007066363.1(LOC105372112):n.642+8466T>C 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 0.157 in 151,956 control chromosomes in the GnomAD database, including 1,920 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 0.16 (1920 hom., cov: 32)
• Consequence: LOC105372112 XR_007066363.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.30

Genes affected

LOC105372112 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.179 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105372112	XR_007066363.1	n.642+8466T>C		intron_variant, non_coding_transcript_variant
LOC105372112	XR_007066364.1	n.887+8466T>C		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.157 AC: 23872 AN: 151838 Hom.: 1917 Cov.: 32

Gnomad AFR AF: 0.182

Gnomad AMI AF: 0.0987

Gnomad AMR AF: 0.168

Gnomad ASJ AF: 0.0986

Gnomad EAS AF: 0.144

Gnomad SAS AF: 0.184

Gnomad FIN AF: 0.126

Gnomad MID AF: 0.171

Gnomad NFE AF: 0.147

Gnomad OTH AF: 0.156

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

GnomAD4 genome AF: 0.157 AC: 23893 AN: 151956 Hom.: 1920 Cov.: 32 AF XY: 0.158 AC XY: 11762 AN XY: 74270

Gnomad4 AFR AF: 0.182

Gnomad4 AMR AF: 0.168

Gnomad4 ASJ AF: 0.0986

Gnomad4 EAS AF: 0.144

Gnomad4 SAS AF: 0.184

Gnomad4 FIN AF: 0.126

Gnomad4 NFE AF: 0.147

Gnomad4 OTH AF: 0.154

Alfa AF: 0.108 Hom.: 210

Bravo AF: 0.162

Asia WGS AF: 0.161 AC: 557 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
Cadd	Benign	0.015
Dann	Benign	0.34

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1943985; hg19: chr18-47235193;