rs2902941

Positions:

• chr20-40462874-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+1446T>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 0.473 in 151,998 control chromosomes in the GnomAD database, including 20,476 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 0.47 (20476 hom., cov: 32)
• Consequence: LOC105372618 XR_936718.3 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.748

Genes affected

LOC105372618 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.808 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC105372618	XR_936718.3	n.1155+1446T>C		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.472 AC: 71708 AN: 151880 Hom.: 20419 Cov.: 32

Gnomad AFR AF: 0.815

Gnomad AMI AF: 0.316

Gnomad AMR AF: 0.387

Gnomad ASJ AF: 0.339

Gnomad EAS AF: 0.283

Gnomad SAS AF: 0.426

Gnomad FIN AF: 0.245

Gnomad MID AF: 0.329

Gnomad NFE AF: 0.346

Gnomad OTH AF: 0.429

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

GnomAD4 genome AF: 0.473 AC: 71823 AN: 151998 Hom.: 20476 Cov.: 32 AF XY: 0.464 AC XY: 34450 AN XY: 74316

Gnomad4 AFR AF: 0.815

Gnomad4 AMR AF: 0.387

Gnomad4 ASJ AF: 0.339

Gnomad4 EAS AF: 0.284

Gnomad4 SAS AF: 0.426

Gnomad4 FIN AF: 0.245

Gnomad4 NFE AF: 0.346

Gnomad4 OTH AF: 0.428

Alfa AF: 0.382 Hom.: 5540

Bravo AF: 0.496

Asia WGS AF: 0.388 AC: 1346 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.67
DANN	Benign	0.64

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2902941; hg19: chr20-39091514;