rs10501858

Positions:

• chr11-126160720-G-A
• chr11-126160720-G-C

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The ENST00000532357.1(ENSG00000254833):​n.7G>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 0.0778 in 152,318 control chromosomes in the GnomAD database, including 674 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 0.078 (673 hom., cov: 33)
  • Exomes 𝑓: 0.033 (1 hom.)
• Consequence: ENSG00000254833 ENST00000532357.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.06

Genes affected

ENSG00000254833 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.34).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.164 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.126160720G>A		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000254833	ENST00000532357.1	n.7G>A		non_coding_transcript_exon_variant	1/2	4

Frequencies

GnomAD3 genomes AF: 0.0778 AC: 11840 AN: 152140 Hom.: 671 Cov.: 33

Gnomad AFR AF: 0.0255

Gnomad AMI AF: 0.0560

Gnomad AMR AF: 0.169

Gnomad ASJ AF: 0.150

Gnomad EAS AF: 0.0856

Gnomad SAS AF: 0.142

Gnomad FIN AF: 0.0989

Gnomad MID AF: 0.127

Gnomad NFE AF: 0.0767

Gnomad OTH AF: 0.0936

GnomAD4 exome AF: 0.0333 AC: 2 AN: 60 Hom.: 1 Cov.: 0 AF XY: 0.0556 AC XY: 2 AN XY: 36

Gnomad4 AFR exome AF: 0.00

Gnomad4 EAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.100

Gnomad4 NFE exome AF: 0.00

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome AF: 0.0779 AC: 11854 AN: 152258 Hom.: 673 Cov.: 33 AF XY: 0.0816 AC XY: 6076 AN XY: 74450

Gnomad4 AFR AF: 0.0256

Gnomad4 AMR AF: 0.169

Gnomad4 ASJ AF: 0.150

Gnomad4 EAS AF: 0.0855

Gnomad4 SAS AF: 0.142

Gnomad4 FIN AF: 0.0989

Gnomad4 NFE AF: 0.0767

Gnomad4 OTH AF: 0.0959

Alfa AF: 0.0843 Hom.: 300

Bravo AF: 0.0830

Asia WGS AF: 0.135 AC: 469 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.34
CADD	Benign	18
DANN	Benign	0.89

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10501858; hg19: chr11-126030615;