rs852069

Positions:

• chr20-17141948-A-G
• chr20-17141948-A-T

Variant summary

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

The XR_937289.1(LOC105372544):​n.310+6816A>G 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 0.562 in 151,956 control chromosomes in the GnomAD database, including 24,759 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 0.56 (24759 hom., cov: 32)
• Consequence: LOC105372544 XR_937289.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.10

Genes affected

LOC105372544 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.626 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC105372544	XR_937289.1	n.310+6816A>G		intron_variant, non_coding_transcript_variant
LOC105372544	XR_937288.2	n.310+6816A>G		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.563 AC: 85420 AN: 151838 Hom.: 24759 Cov.: 32

Gnomad AFR AF: 0.494

Gnomad AMI AF: 0.400

Gnomad AMR AF: 0.532

Gnomad ASJ AF: 0.645

Gnomad EAS AF: 0.219

Gnomad SAS AF: 0.365

Gnomad FIN AF: 0.673

Gnomad MID AF: 0.525

Gnomad NFE AF: 0.631

Gnomad OTH AF: 0.595

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

GnomAD4 genome AF: 0.562 AC: 85438 AN: 151956 Hom.: 24759 Cov.: 32 AF XY: 0.559 AC XY: 41540 AN XY: 74286

Gnomad4 AFR AF: 0.493

Gnomad4 AMR AF: 0.532

Gnomad4 ASJ AF: 0.645

Gnomad4 EAS AF: 0.219

Gnomad4 SAS AF: 0.365

Gnomad4 FIN AF: 0.673

Gnomad4 NFE AF: 0.631

Gnomad4 OTH AF: 0.595

Alfa AF: 0.606 Hom.: 61682

Bravo AF: 0.550

Asia WGS AF: 0.339 AC: 1182 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	6.7
DANN	Benign	0.65

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs852069; hg19: chr20-17122593;