chr18-31252224-T-C

Position:

• chr18-31252224-T-C

Variant summary

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

The XR_001753388.2(LOC105372049):​n.391+1055T>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 0.414 in 151,944 control chromosomes in the GnomAD database, including 14,067 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 0.41 (14067 hom., cov: 32)
• Consequence: LOC105372049 XR_001753388.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.395

Genes affected

LOC105372049 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.486 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC105372049	XR_001753388.2	n.391+1055T>C		intron_variant, non_coding_transcript_variant
LOC105372049	XR_935334.3	n.1446T>C		non_coding_transcript_exon_variant	3/3

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.414 AC: 62832 AN: 151826 Hom.: 14077 Cov.: 32

Gnomad AFR AF: 0.287

Gnomad AMI AF: 0.383

Gnomad AMR AF: 0.324

Gnomad ASJ AF: 0.495

Gnomad EAS AF: 0.180

Gnomad SAS AF: 0.447

Gnomad FIN AF: 0.621

Gnomad MID AF: 0.472

Gnomad NFE AF: 0.490

Gnomad OTH AF: 0.440

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

GnomAD4 genome AF: 0.414 AC: 62830 AN: 151944 Hom.: 14067 Cov.: 32 AF XY: 0.419 AC XY: 31088 AN XY: 74264

Gnomad4 AFR AF: 0.286

Gnomad4 AMR AF: 0.323

Gnomad4 ASJ AF: 0.495

Gnomad4 EAS AF: 0.180

Gnomad4 SAS AF: 0.446

Gnomad4 FIN AF: 0.621

Gnomad4 NFE AF: 0.490

Gnomad4 OTH AF: 0.440

Alfa AF: 0.460 Hom.: 2054

Bravo AF: 0.382

Asia WGS AF: 0.322 AC: 1111 AN: 3456

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.11
DANN	Benign	0.75

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7231460; hg19: chr18-28832187;