rs2143877

Variant names:

• chr20-40464255-A-G
• rs2143877
• XR_936718.3:n.1155+65T>C

Variant summary

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

The XR_936718.3(LOC105372618):​n.1155+65T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.333 in 152,176 control chromosomes in the GnomAD database, including 9,123 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 0.33 (9123 hom., cov: 33)
• Consequence: LOC105372618 XR_936718.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0520
• Publications: 10 publications found

Genes affected

LOC105372618 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.463 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105372618	XR_936718.3	n.1155+65T>C		intron_variant	Intron 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.333 AC: 50685 AN: 152058 Hom.: 9109 Cov.: 33

Gnomad AFR AF: 0.468

Gnomad AMI AF: 0.246

Gnomad AMR AF: 0.296

Gnomad ASJ AF: 0.173

Gnomad EAS AF: 0.269

Gnomad SAS AF: 0.320

Gnomad FIN AF: 0.201

Gnomad MID AF: 0.149

Gnomad NFE AF: 0.297

Gnomad OTH AF: 0.298

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

GnomAD4 genome AF: 0.333 AC: 50741 AN: 152176 Hom.: 9123 Cov.: 33 AF XY: 0.326 AC XY: 24244 AN XY: 74402

African (AFR) AF: 0.468 AC: 19429 AN: 41512

American (AMR) AF: 0.296 AC: 4524 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.173 AC: 602 AN: 3470

East Asian (EAS) AF: 0.270 AC: 1401 AN: 5180

South Asian (SAS) AF: 0.321 AC: 1548 AN: 4824

European-Finnish (FIN) AF: 0.201 AC: 2131 AN: 10590

Middle Eastern (MID) AF: 0.146 AC: 43 AN: 294

European-Non Finnish (NFE) AF: 0.297 AC: 20218 AN: 67990

Other (OTH) AF: 0.294 AC: 621 AN: 2114

Alfa AF: 0.307 Hom.: 19205

Bravo AF: 0.345

Asia WGS AF: 0.309 AC: 1073 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	1.6
DANN	Benign	0.30
PhyloP100		0.052

Splicing

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

Other links and lift over

dbSNP: rs2143877; hg19: chr20-39092895;