rs740586

chr19-43692379-C-T

Variant summary

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

The NR_172891.1(LOC105372412):n.924C>T 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 0.193 in 152,048 control chromosomes in the GnomAD database, including 3,148 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 0.19 (3148 hom., cov: 31)
  • Exomes 𝑓: 0.091 (0 hom.)
• Consequence: LOC105372412 NR_172891.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -4.18

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 (EAS) allele frequency at 95% confidence interval = 0.348 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105372412	NR_172891.1	n.924C>T		non_coding_transcript_exon_variant	3/7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000636801.1	n.258C>T		non_coding_transcript_exon_variant	2/6
	ENST00000637093.1	n.98C>T		non_coding_transcript_exon_variant	1/5	5

Frequencies

GnomAD3 genomes AF: 0.193 AC: 29385 AN: 151886 Hom.: 3148 Cov.: 31

Gnomad AFR AF: 0.0949

Gnomad AMI AF: 0.209

Gnomad AMR AF: 0.247

Gnomad ASJ AF: 0.120

Gnomad EAS AF: 0.361

Gnomad SAS AF: 0.162

Gnomad FIN AF: 0.234

Gnomad MID AF: 0.158

Gnomad NFE AF: 0.228

Gnomad OTH AF: 0.199

GnomAD4 exome AF: 0.0909 AC: 4 AN: 44 Hom.: 0 Cov.: 0 AF XY: 0.125 AC XY: 4 AN XY: 32

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.150

Gnomad4 OTH exome AF: 0.125

GnomAD4 genome AF: 0.193 AC: 29381 AN: 152004 Hom.: 3148 Cov.: 31 AF XY: 0.195 AC XY: 14469 AN XY: 74296

Gnomad4 AFR AF: 0.0948

Gnomad4 AMR AF: 0.247

Gnomad4 ASJ AF: 0.120

Gnomad4 EAS AF: 0.362

Gnomad4 SAS AF: 0.161

Gnomad4 FIN AF: 0.234

Gnomad4 NFE AF: 0.228

Gnomad4 OTH AF: 0.199

Alfa AF: 0.201 Hom.: 866

Bravo AF: 0.189

Asia WGS AF: 0.245 AC: 852 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	0.045
Dann	Benign	0.58

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs740586; hg19: chr19-44196531;