18-79013973-C-T

Position:

• chr18-79013973-C-T

Variant summary

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

The XR_001753514.2(LOC105372225):​n.226+9915G>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 0.373 in 152,102 control chromosomes in the GnomAD database, including 11,421 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 0.37 (11421 hom., cov: 34)
• Consequence: LOC105372225 XR_001753514.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0710

Genes affected

LOC105372225 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.529 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC105372225	XR_001753514.2	n.226+9915G>A		intron_variant, non_coding_transcript_variant
LOC105372225	XR_001753513.2	n.338+9915G>A		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.373 AC: 56744 AN: 151984 Hom.: 11402 Cov.: 34

Gnomad AFR AF: 0.535

Gnomad AMI AF: 0.382

Gnomad AMR AF: 0.316

Gnomad ASJ AF: 0.326

Gnomad EAS AF: 0.400

Gnomad SAS AF: 0.344

Gnomad FIN AF: 0.299

Gnomad MID AF: 0.278

Gnomad NFE AF: 0.303

Gnomad OTH AF: 0.361

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

GnomAD4 genome AF: 0.373 AC: 56805 AN: 152102 Hom.: 11421 Cov.: 34 AF XY: 0.374 AC XY: 27796 AN XY: 74348

Gnomad4 AFR AF: 0.535

Gnomad4 AMR AF: 0.316

Gnomad4 ASJ AF: 0.326

Gnomad4 EAS AF: 0.401

Gnomad4 SAS AF: 0.343

Gnomad4 FIN AF: 0.299

Gnomad4 NFE AF: 0.303

Gnomad4 OTH AF: 0.359

Alfa AF: 0.319 Hom.: 8055

Bravo AF: 0.382

Asia WGS AF: 0.370 AC: 1283 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	0.73
DANN	Benign	0.46

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7241993; hg19: chr18-76773973;