chr20-17155501-C-T

Position:

• chr20-17155501-C-T

Variant summary

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

The XR_937289.1(LOC105372544):​n.311-18378C>T 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 0.632 in 151,898 control chromosomes in the GnomAD database, including 32,398 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 0.63 (32398 hom., cov: 30)
• Consequence: LOC105372544 XR_937289.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.500

Genes affected

LOC105372544 (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 (NFE) allele frequency at 95% confidence interval = 0.754 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC105372544	XR_937289.1	n.311-18378C>T		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.633 AC: 96043 AN: 151782 Hom.: 32397 Cov.: 30

Gnomad AFR AF: 0.388

Gnomad AMI AF: 0.608

Gnomad AMR AF: 0.616

Gnomad ASJ AF: 0.706

Gnomad EAS AF: 0.578

Gnomad SAS AF: 0.583

Gnomad FIN AF: 0.820

Gnomad MID AF: 0.557

Gnomad NFE AF: 0.760

Gnomad OTH AF: 0.658

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

GnomAD4 genome AF: 0.632 AC: 96065 AN: 151898 Hom.: 32398 Cov.: 30 AF XY: 0.633 AC XY: 46987 AN XY: 74240

Gnomad4 AFR AF: 0.388

Gnomad4 AMR AF: 0.616

Gnomad4 ASJ AF: 0.706

Gnomad4 EAS AF: 0.577

Gnomad4 SAS AF: 0.583

Gnomad4 FIN AF: 0.820

Gnomad4 NFE AF: 0.760

Gnomad4 OTH AF: 0.657

Alfa AF: 0.626 Hom.: 3110

Bravo AF: 0.608

Asia WGS AF: 0.545 AC: 1898 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	2.5
DANN	Benign	0.82

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs708983; hg19: chr20-17136146;