rs116909374

Positions:

• chr14-36269155-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The XR_007064116.1(LOC124903302):​n.1021G>A 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 0.023 in 152,260 control chromosomes in the GnomAD database, including 67 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 0.023 (67 hom., cov: 32)
• Consequence: LOC124903302 XR_007064116.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.749

Genes affected

LOC124903302 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.5).
• BS1: Variant frequency is greater than expected in population nfe. gnomad4 allele frequency = 0.023 (3495/152260) while in subpopulation NFE AF= 0.0348 (2370/68026). AF 95% confidence interval is 0.0337. There are 67 homozygotes in gnomad4. There are 1689 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
• BS2: High Homozygotes in GnomAd4 at 67 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC124903302	XR_007064116.1	n.1021G>A		non_coding_transcript_exon_variant	2/2

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.0230 AC: 3496 AN: 152142 Hom.: 67 Cov.: 32

Gnomad AFR AF: 0.00719

Gnomad AMI AF: 0.0471

Gnomad AMR AF: 0.0184

Gnomad ASJ AF: 0.0239

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00476

Gnomad FIN AF: 0.0293

Gnomad MID AF: 0.0443

Gnomad NFE AF: 0.0349

Gnomad OTH AF: 0.0344

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

GnomAD4 genome AF: 0.0230 AC: 3495 AN: 152260 Hom.: 67 Cov.: 32 AF XY: 0.0227 AC XY: 1689 AN XY: 74438

Gnomad4 AFR AF: 0.00717

Gnomad4 AMR AF: 0.0184

Gnomad4 ASJ AF: 0.0239

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.00477

Gnomad4 FIN AF: 0.0293

Gnomad4 NFE AF: 0.0348

Gnomad4 OTH AF: 0.0340

Alfa AF: 0.0320 Hom.: 40

Bravo AF: 0.0227

Asia WGS AF: 0.00520 AC: 19 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.50
CADD	Benign	15
DANN	Benign	0.83

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs116909374; hg19: chr14-36738361; COSMIC: COSV52393761;