rs1108567

Variant names:

• chr2-148526499-C-T
• rs1108567
• XR_007087259.1:n.4906C>T

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 11 publications found

Genes affected

LOC124907896 (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 = 0.786 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC124907896	XR_007087259.1	n.4906C>T		non_coding_transcript_exon_variant	Exon 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.789 AC: 32620 AN: 41348

American (AMR) AF: 0.653 AC: 9955 AN: 15250

Ashkenazi Jewish (ASJ) AF: 0.716 AC: 2483 AN: 3470

East Asian (EAS) AF: 0.291 AC: 1488 AN: 5112

South Asian (SAS) AF: 0.564 AC: 2694 AN: 4778

European-Finnish (FIN) AF: 0.780 AC: 8215 AN: 10532

Middle Eastern (MID) AF: 0.847 AC: 249 AN: 294

European-Non Finnish (NFE) AF: 0.792 AC: 53773 AN: 67914

Other (OTH) AF: 0.757 AC: 1595 AN: 2108

Alfa AF: 0.773 Hom.: 59482

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
PhyloP100		-0.48

Splicing

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

Other links and lift over

dbSNP: rs1108567; hg19: chr2-149284068;