rs2140887

Variant names:

• chr11-28019800-A-G
• rs2140887
• XR_007062636.1:n.621T>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The XR_007062636.1(LOC124902655):​n.621T>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 0.464 in 152,062 control chromosomes in the GnomAD database, including 17,893 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 0.46 (17893 hom., cov: 32)
• Consequence: LOC124902655 XR_007062636.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.388
• Publications: 1 publications found

Genes affected

LOC124902655 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.551 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC124902655	XR_007062636.1	n.621T>C		non_coding_transcript_exon_variant	Exon 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000255094	ENST00000525309.1	n.-225T>C		upstream_gene_variant		2

Frequencies

GnomAD3 genomes AF: 0.464 AC: 70487 AN: 151942 Hom.: 17879 Cov.: 32

Gnomad AFR AF: 0.257

Gnomad AMI AF: 0.657

Gnomad AMR AF: 0.560

Gnomad ASJ AF: 0.587

Gnomad EAS AF: 0.277

Gnomad SAS AF: 0.446

Gnomad FIN AF: 0.601

Gnomad MID AF: 0.494

Gnomad NFE AF: 0.553

Gnomad OTH AF: 0.487

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

GnomAD4 genome AF: 0.464 AC: 70539 AN: 152062 Hom.: 17893 Cov.: 32 AF XY: 0.465 AC XY: 34537 AN XY: 74290

African (AFR) AF: 0.257 AC: 10676 AN: 41506

American (AMR) AF: 0.561 AC: 8558 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.587 AC: 2037 AN: 3470

East Asian (EAS) AF: 0.277 AC: 1429 AN: 5160

South Asian (SAS) AF: 0.448 AC: 2161 AN: 4820

European-Finnish (FIN) AF: 0.601 AC: 6338 AN: 10546

Middle Eastern (MID) AF: 0.490 AC: 144 AN: 294

European-Non Finnish (NFE) AF: 0.552 AC: 37560 AN: 67982

Other (OTH) AF: 0.491 AC: 1037 AN: 2110

Alfa AF: 0.523 Hom.: 10947

Bravo AF: 0.454

Asia WGS AF: 0.411 AC: 1429 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	6.5
DANN	Benign	0.75
PhyloP100		0.39

Splicing

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

Other links and lift over

dbSNP: rs2140887; hg19: chr11-28041347;