rs2143877

chr20-40464255-A-G

Variant summary

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

The XR_936718.3(LOC105372618):n.1155+65T>C variant causes a intron, non coding transcript 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, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0520

Genes affected

LOC105372618 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt
LOC105372618	XR_936718.3	n.1155+65T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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

Gnomad4 AFR AF: 0.468

Gnomad4 AMR AF: 0.296

Gnomad4 ASJ AF: 0.173

Gnomad4 EAS AF: 0.270

Gnomad4 SAS AF: 0.321

Gnomad4 FIN AF: 0.201

Gnomad4 NFE AF: 0.297

Gnomad4 OTH AF: 0.294

Alfa AF: 0.292 Hom.: 10291

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2143877; hg19: chr20-39092895;