rs6051846

chr20-3423177-C-T

Variant summary

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

The XR_937212.3(LOC105372508):n.104-1099G>A 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 0.335 in 149,640 control chromosomes in the GnomAD database, including 9,195 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 (9195 hom., cov: 30)
• Consequence: LOC105372508 XR_937212.3 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0820

Genes affected

LOC105372508 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.472 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105372508	XR_937212.3	n.104-1099G>A		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.335 AC: 50129 AN: 149582 Hom.: 9186 Cov.: 30

Gnomad AFR AF: 0.478

Gnomad AMI AF: 0.250

Gnomad AMR AF: 0.353

Gnomad ASJ AF: 0.335

Gnomad EAS AF: 0.166

Gnomad SAS AF: 0.168

Gnomad FIN AF: 0.227

Gnomad MID AF: 0.234

Gnomad NFE AF: 0.287

Gnomad OTH AF: 0.331

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

GnomAD4 genome AF: 0.335 AC: 50147 AN: 149640 Hom.: 9195 Cov.: 30 AF XY: 0.330 AC XY: 24049 AN XY: 72896

Gnomad4 AFR AF: 0.478

Gnomad4 AMR AF: 0.353

Gnomad4 ASJ AF: 0.335

Gnomad4 EAS AF: 0.166

Gnomad4 SAS AF: 0.167

Gnomad4 FIN AF: 0.227

Gnomad4 NFE AF: 0.287

Gnomad4 OTH AF: 0.327

Alfa AF: 0.321 Hom.: 1408

Bravo AF: 0.351

Asia WGS AF: 0.171 AC: 595 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
Cadd	Benign	1.1
Dann	Benign	0.34

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6051846; hg19: chr20-3403824;