20-3069074-G-C

Position:

• chr20-3069074-G-C

Variant summary

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

The XR_430278.4(LOC101929098):​n.444C>G variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.485 in 152,150 control chromosomes in the GnomAD database, including 17,982 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 0.48 (17982 hom., cov: 33)
• Consequence: LOC101929098 XR_430278.4 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.393

Genes affected

LOC101929098 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.78).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.509 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC101929098	XR_007067503.1	n.409C>G		non_coding_transcript_exon_variant	2/2
LOC101929098	XR_430278.4	n.444C>G		non_coding_transcript_exon_variant	2/2
		n.3069074G>C		intergenic_region

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.485 AC: 73686 AN: 152032 Hom.: 17960 Cov.: 33

Gnomad AFR AF: 0.504

Gnomad AMI AF: 0.304

Gnomad AMR AF: 0.497

Gnomad ASJ AF: 0.485

Gnomad EAS AF: 0.462

Gnomad SAS AF: 0.526

Gnomad FIN AF: 0.469

Gnomad MID AF: 0.434

Gnomad NFE AF: 0.475

Gnomad OTH AF: 0.444

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

GnomAD4 genome AF: 0.485 AC: 73759 AN: 152150 Hom.: 17982 Cov.: 33 AF XY: 0.485 AC XY: 36071 AN XY: 74376

Gnomad4 AFR AF: 0.504

Gnomad4 AMR AF: 0.498

Gnomad4 ASJ AF: 0.485

Gnomad4 EAS AF: 0.462

Gnomad4 SAS AF: 0.526

Gnomad4 FIN AF: 0.469

Gnomad4 NFE AF: 0.475

Gnomad4 OTH AF: 0.446

Alfa AF: 0.349 Hom.: 914

Bravo AF: 0.487

Asia WGS AF: 0.560 AC: 1950 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
CADD	Benign	6.1
DANN	Benign	0.63

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4813625; hg19: chr20-3049720;