rs10493090

chr1-40161246-G-T

Variant summary

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

The XR_947232.3(LOC105378671):n.33C>A 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 0.0961 in 1,025,584 control chromosomes in the GnomAD database, including 5,061 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 0.090 (705 hom., cov: 32)
  • Exomes 𝑓: 0.097 (4356 hom.)
• Consequence: LOC105378671 XR_947232.3 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.233

Genes affected

LOC105378671 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.67).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.144 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105378671	XR_947232.3	n.33C>A		non_coding_transcript_exon_variant	1/3

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.0898 AC: 13667 AN: 152150 Hom.: 703 Cov.: 32

Gnomad AFR AF: 0.0646

Gnomad AMI AF: 0.0428

Gnomad AMR AF: 0.130

Gnomad ASJ AF: 0.0565

Gnomad EAS AF: 0.152

Gnomad SAS AF: 0.153

Gnomad FIN AF: 0.0932

Gnomad MID AF: 0.0854

Gnomad NFE AF: 0.0891

Gnomad OTH AF: 0.0842

GnomAD4 exome AF: 0.0971 AC: 84839 AN: 873316 Hom.: 4356 AF XY: 0.0975 AC XY: 42001 AN XY: 430626

Gnomad4 AFR exome AF: 0.0610

Gnomad4 AMR exome AF: 0.113

Gnomad4 ASJ exome AF: 0.0565

Gnomad4 EAS exome AF: 0.118

Gnomad4 SAS exome AF: 0.142

Gnomad4 FIN exome AF: 0.0902

Gnomad4 NFE exome AF: 0.0954

Gnomad4 OTH exome AF: 0.0976

GnomAD4 genome AF: 0.0899 AC: 13689 AN: 152268 Hom.: 705 Cov.: 32 AF XY: 0.0918 AC XY: 6832 AN XY: 74442

Gnomad4 AFR AF: 0.0645

Gnomad4 AMR AF: 0.130

Gnomad4 ASJ AF: 0.0565

Gnomad4 EAS AF: 0.151

Gnomad4 SAS AF: 0.153

Gnomad4 FIN AF: 0.0932

Gnomad4 NFE AF: 0.0891

Gnomad4 OTH AF: 0.0881

Alfa AF: 0.0908 Hom.: 955

Bravo AF: 0.0915

Asia WGS AF: 0.130 AC: 454 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.67
Cadd	Benign	4.8
Dann	Benign	0.80

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10493090; hg19: chr1-40626918;