rs346054

chr19-43700317-G-C

Variant summary

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

The NR_172891.1(LOC105372412):n.2178G>C 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 0.471 in 152,154 control chromosomes in the GnomAD database, including 17,944 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 0.47 (17928 hom., cov: 33)
  • Exomes 𝑓: 0.59 (16 hom.)
• Consequence: LOC105372412 NR_172891.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.12

Genes affected

(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 = 0.546 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105372412	NR_172891.1	n.2178G>C		non_coding_transcript_exon_variant	7/7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000636801.1	n.1512G>C		non_coding_transcript_exon_variant	6/6
	ENST00000637093.1	n.1352G>C		non_coding_transcript_exon_variant	5/5	5

Frequencies

GnomAD3 genomes AF: 0.471 AC: 71583 AN: 151944 Hom.: 17921 Cov.: 33

Gnomad AFR AF: 0.289

Gnomad AMI AF: 0.628

Gnomad AMR AF: 0.521

Gnomad ASJ AF: 0.456

Gnomad EAS AF: 0.472

Gnomad SAS AF: 0.517

Gnomad FIN AF: 0.566

Gnomad MID AF: 0.471

Gnomad NFE AF: 0.550

Gnomad OTH AF: 0.492

GnomAD4 exome AF: 0.589 AC: 53 AN: 90 Hom.: 16 Cov.: 0 AF XY: 0.553 AC XY: 42 AN XY: 76

Gnomad4 ASJ exome AF: 0.500

Gnomad4 EAS exome AF: 0.500

Gnomad4 SAS exome AF: 0.500

Gnomad4 FIN exome AF: 0.750

Gnomad4 NFE exome AF: 0.571

Gnomad4 OTH exome AF: 0.500

GnomAD4 genome AF: 0.471 AC: 71623 AN: 152064 Hom.: 17928 Cov.: 33 AF XY: 0.473 AC XY: 35140 AN XY: 74312

Gnomad4 AFR AF: 0.290

Gnomad4 AMR AF: 0.521

Gnomad4 ASJ AF: 0.456

Gnomad4 EAS AF: 0.473

Gnomad4 SAS AF: 0.516

Gnomad4 FIN AF: 0.566

Gnomad4 NFE AF: 0.550

Gnomad4 OTH AF: 0.492

Alfa AF: 0.504 Hom.: 2499

Bravo AF: 0.457

Asia WGS AF: 0.495 AC: 1723 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	5.8
Dann	Benign	0.59

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs346054; hg19: chr19-44204469;