11-126160720-G-A

Variant names:

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

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 4 publications found

Genes affected

ENSG00000254833 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000532357.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000254833	ENST00000532357.1	TSL:4	n.7G>A		non_coding_transcript_exon	Exon 1 of 2

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

African (AFR) AF: 0.00 AC: 0 AN: 2

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AF: 0.00 AC: 0 AN: 4

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AF: 0.100 AC: 2 AN: 20

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 32

Other (OTH) AF: 0.00 AC: 0 AN: 2

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

African (AFR) AF: 0.0256 AC: 1064 AN: 41552

American (AMR) AF: 0.169 AC: 2588 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.150 AC: 520 AN: 3472

East Asian (EAS) AF: 0.0855 AC: 442 AN: 5172

South Asian (SAS) AF: 0.142 AC: 685 AN: 4832

European-Finnish (FIN) AF: 0.0989 AC: 1048 AN: 10598

Middle Eastern (MID) AF: 0.116 AC: 34 AN: 294

European-Non Finnish (NFE) AF: 0.0767 AC: 5219 AN: 68028

Other (OTH) AF: 0.0959 AC: 203 AN: 2116

Alfa AF: 0.0795 Hom.: 509

Bravo AF: 0.0830

Asia WGS AF: 0.135 AC: 469 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.34
CADD	Benign	18
DANN	Benign	0.89
PhyloP100		2.1

Splicing

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

Other links and lift over

dbSNP: rs10501858; hg19: chr11-126030615;