rs966376

Variant names:

• chr18-31252875-T-C
• rs966376
• XR_935334.3:n.2097T>C

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 2 publications found

Genes affected

LOC105372049 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
LOC105372049	XR_935334.3	n.2097T>C		non_coding_transcript_exon_variant	Exon 3 of 3
LOC105372049	XR_001753388.2	n.391+1706T>C		intron_variant	Intron 3 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000293651	ENST00000716842.1	n.285+2431T>C		intron_variant	Intron 2 of 2
ENSG00000293651	ENST00000716843.1	n.212+2431T>C		intron_variant	Intron 2 of 2

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

African (AFR) AF: 0.286 AC: 11861 AN: 41438

American (AMR) AF: 0.324 AC: 4935 AN: 15248

Ashkenazi Jewish (ASJ) AF: 0.496 AC: 1721 AN: 3472

East Asian (EAS) AF: 0.137 AC: 708 AN: 5174

South Asian (SAS) AF: 0.445 AC: 2141 AN: 4812

European-Finnish (FIN) AF: 0.620 AC: 6535 AN: 10536

Middle Eastern (MID) AF: 0.463 AC: 136 AN: 294

European-Non Finnish (NFE) AF: 0.490 AC: 33290 AN: 67946

Other (OTH) AF: 0.438 AC: 925 AN: 2114

Alfa AF: 0.470 Hom.: 23100

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
PhyloP100		-2.5

Splicing

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

Other links and lift over

dbSNP: rs966376; hg19: chr18-28832838;