20-40462847-A-G

Position:

• chr20-40462847-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+1473T>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 0.342 in 152,018 control chromosomes in the GnomAD database, including 9,682 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 0.34 (9682 hom., cov: 32)
• Consequence: LOC105372618 XR_936718.3 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0610

Genes affected

LOC105372618 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.62).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.491 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC105372618	XR_936718.3	n.1155+1473T>C		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.341 AC: 51856 AN: 151900 Hom.: 9662 Cov.: 32

Gnomad AFR AF: 0.497

Gnomad AMI AF: 0.246

Gnomad AMR AF: 0.299

Gnomad ASJ AF: 0.170

Gnomad EAS AF: 0.270

Gnomad SAS AF: 0.320

Gnomad FIN AF: 0.201

Gnomad MID AF: 0.152

Gnomad NFE AF: 0.297

Gnomad OTH AF: 0.304

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

GnomAD4 genome AF: 0.342 AC: 51917 AN: 152018 Hom.: 9682 Cov.: 32 AF XY: 0.334 AC XY: 24790 AN XY: 74310

Gnomad4 AFR AF: 0.497

Gnomad4 AMR AF: 0.299

Gnomad4 ASJ AF: 0.170

Gnomad4 EAS AF: 0.272

Gnomad4 SAS AF: 0.321

Gnomad4 FIN AF: 0.201

Gnomad4 NFE AF: 0.297

Gnomad4 OTH AF: 0.300

Alfa AF: 0.291 Hom.: 6536

Bravo AF: 0.354

Asia WGS AF: 0.312 AC: 1084 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.62
CADD	Benign	12
DANN	Benign	0.91

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2902940; hg19: chr20-39091487;