rs2140887

Positions:

• chr11-28019800-A-G

Variant summary

Our verdict is Benign. Variant got -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

Genes affected

LOC124902655 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt
LOC124902655	XR_007062636.1	n.621T>C		non_coding_transcript_exon_variant	1/2

Ensembl

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

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

Gnomad4 AFR AF: 0.257

Gnomad4 AMR AF: 0.561

Gnomad4 ASJ AF: 0.587

Gnomad4 EAS AF: 0.277

Gnomad4 SAS AF: 0.448

Gnomad4 FIN AF: 0.601

Gnomad4 NFE AF: 0.552

Gnomad4 OTH AF: 0.491

Alfa AF: 0.523 Hom.: 9760

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2140887; hg19: chr11-28041347;