rs878198

Positions:

• chr20-48563115-C-A

Variant summary

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

The XR_936817.4(LOC105372646):​n.342+168G>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 0.646 in 152,010 control chromosomes in the GnomAD database, including 32,547 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 0.65 (32547 hom., cov: 32)
• Consequence: LOC105372646 XR_936817.4 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.103

Genes affected

LOC105372646 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.719 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC105372646	XR_936817.4	n.342+168G>T		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.645 AC: 98036 AN: 151890 Hom.: 32506 Cov.: 32

Gnomad AFR AF: 0.496

Gnomad AMI AF: 0.776

Gnomad AMR AF: 0.730

Gnomad ASJ AF: 0.693

Gnomad EAS AF: 0.626

Gnomad SAS AF: 0.566

Gnomad FIN AF: 0.769

Gnomad MID AF: 0.585

Gnomad NFE AF: 0.702

Gnomad OTH AF: 0.631

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

GnomAD4 genome AF: 0.646 AC: 98133 AN: 152010 Hom.: 32547 Cov.: 32 AF XY: 0.649 AC XY: 48240 AN XY: 74312

Gnomad4 AFR AF: 0.496

Gnomad4 AMR AF: 0.730

Gnomad4 ASJ AF: 0.693

Gnomad4 EAS AF: 0.626

Gnomad4 SAS AF: 0.565

Gnomad4 FIN AF: 0.769

Gnomad4 NFE AF: 0.702

Gnomad4 OTH AF: 0.636

Alfa AF: 0.671 Hom.: 20014

Bravo AF: 0.640

Asia WGS AF: 0.626 AC: 2178 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.1
DANN	Benign	0.45

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs878198; hg19: chr20-47179653;