rs3810171

Positions:

• chr19-41193088-C-T

Variant summary

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

The 19-41193088-C-T variant causes a upstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0802 in 1,015,514 control chromosomes in the GnomAD database, including 3,836 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 0.10 (859 hom., cov: 32)
  • Exomes 𝑓: 0.077 (2977 hom.)
• Consequence: LOC124904790 XM_047439802.1 upstream_gene
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.143

Genes affected

LOC124904790 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.76).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.145 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC124904790	XM_047439802.1			upstream_gene_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.100 AC: 15230 AN: 152040 Hom.: 856 Cov.: 32

Gnomad AFR AF: 0.134

Gnomad AMI AF: 0.102

Gnomad AMR AF: 0.0900

Gnomad ASJ AF: 0.125

Gnomad EAS AF: 0.154

Gnomad SAS AF: 0.121

Gnomad FIN AF: 0.0661

Gnomad MID AF: 0.0981

Gnomad NFE AF: 0.0805

Gnomad OTH AF: 0.0979

GnomAD4 exome AF: 0.0767 AC: 66198 AN: 863356 Hom.: 2977 Cov.: 12 AF XY: 0.0782 AC XY: 33284 AN XY: 425432

Gnomad4 AFR exome AF: 0.115

Gnomad4 AMR exome AF: 0.0853

Gnomad4 ASJ exome AF: 0.120

Gnomad4 EAS exome AF: 0.161

Gnomad4 SAS exome AF: 0.103

Gnomad4 FIN exome AF: 0.0739

Gnomad4 NFE exome AF: 0.0693

Gnomad4 OTH exome AF: 0.0849

GnomAD4 genome AF: 0.100 AC: 15253 AN: 152158 Hom.: 859 Cov.: 32 AF XY: 0.102 AC XY: 7558 AN XY: 74380

Gnomad4 AFR AF: 0.134

Gnomad4 AMR AF: 0.0899

Gnomad4 ASJ AF: 0.125

Gnomad4 EAS AF: 0.154

Gnomad4 SAS AF: 0.120

Gnomad4 FIN AF: 0.0661

Gnomad4 NFE AF: 0.0805

Gnomad4 OTH AF: 0.0974

Alfa AF: 0.0924 Hom.: 83

Bravo AF: 0.106

Asia WGS AF: 0.147 AC: 513 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.76
CADD	Benign	7.3
DANN	Benign	0.95

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs3810171; hg19: chr19-41698993;