rs10501858

Variant names:

• chr11-126160720-G-A
• rs10501858
• ENST00000532357.1:n.7G>A

Your query was ambiguous. Multiple possible variants found:

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

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000254833	ENST00000532357.1	n.7G>A		non_coding_transcript_exon_variant	Exon 1 of 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;