rs1108567

Positions:

• chr2-148526499-C-T

Variant summary

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

The XR_007087259.1(LOC124907896):​n.4906C>T 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 0.751 in 151,716 control chromosomes in the GnomAD database, including 43,814 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 0.75 (43814 hom., cov: 29)
• Consequence: LOC124907896 XR_007087259.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.482

Genes affected

LOC124907896 (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 = 0.786 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC124907896	XR_007087259.1	n.4906C>T		non_coding_transcript_exon_variant	2/2

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.751 AC: 113854 AN: 151598 Hom.: 43799 Cov.: 29

Gnomad AFR AF: 0.789

Gnomad AMI AF: 0.921

Gnomad AMR AF: 0.654

Gnomad ASJ AF: 0.716

Gnomad EAS AF: 0.291

Gnomad SAS AF: 0.564

Gnomad FIN AF: 0.780

Gnomad MID AF: 0.845

Gnomad NFE AF: 0.792

Gnomad OTH AF: 0.764

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

GnomAD4 genome AF: 0.751 AC: 113910 AN: 151716 Hom.: 43814 Cov.: 29 AF XY: 0.744 AC XY: 55115 AN XY: 74122

Gnomad4 AFR AF: 0.789

Gnomad4 AMR AF: 0.653

Gnomad4 ASJ AF: 0.716

Gnomad4 EAS AF: 0.291

Gnomad4 SAS AF: 0.564

Gnomad4 FIN AF: 0.780

Gnomad4 NFE AF: 0.792

Gnomad4 OTH AF: 0.757

Alfa AF: 0.775 Hom.: 46035

Bravo AF: 0.740

Asia WGS AF: 0.444 AC: 1546 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	1.7
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: rs1108567; hg19: chr2-149284068;