rs966376

Positions:

• chr18-31252875-T-C

Variant summary

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

The XR_935334.3(LOC105372049):​n.2097T>C variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.412 in 151,946 control chromosomes in the GnomAD database, including 14,037 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 (14037 hom., cov: 32)
• Consequence: LOC105372049 XR_935334.3 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.50

Genes affected

LOC105372049 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• 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_935334.3	n.2097T>C		non_coding_transcript_exon_variant	3/3
		n.31252875T>C		intergenic_region
LOC105372049	XR_001753388.2	n.391+1706T>C		intron_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.412 AC: 62605 AN: 151828 Hom.: 14046 Cov.: 32

Gnomad AFR AF: 0.287

Gnomad AMI AF: 0.385

Gnomad AMR AF: 0.324

Gnomad ASJ AF: 0.496

Gnomad EAS AF: 0.137

Gnomad SAS AF: 0.447

Gnomad FIN AF: 0.620

Gnomad MID AF: 0.472

Gnomad NFE AF: 0.490

Gnomad OTH AF: 0.438

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

GnomAD4 genome AF: 0.412 AC: 62603 AN: 151946 Hom.: 14037 Cov.: 32 AF XY: 0.417 AC XY: 30943 AN XY: 74246

Gnomad4 AFR AF: 0.286

Gnomad4 AMR AF: 0.324

Gnomad4 ASJ AF: 0.496

Gnomad4 EAS AF: 0.137

Gnomad4 SAS AF: 0.445

Gnomad4 FIN AF: 0.620

Gnomad4 NFE AF: 0.490

Gnomad4 OTH AF: 0.438

Alfa AF: 0.472 Hom.: 16827

Bravo AF: 0.380

Asia WGS AF: 0.316 AC: 1098 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.27
DANN	Benign	0.73

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs966376; hg19: chr18-28832838;