11-118709156-G-A

Variant names:

• chr11-118709156-G-A
• rs10892258
• ENST00000646572.2:n.1235G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000646572.2(ENSG00000255422):​n.1235G>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 0.195 in 152,074 control chromosomes in the GnomAD database, including 3,229 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 0.20 (3229 hom., cov: 32)
• Consequence: ENSG00000255422 ENST00000646572.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.365
• Publications: 33 publications found

Genes affected

ENSG00000255422 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.285 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000646572.2. 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
	ENSG00000255422	ENST00000646572.2		n.1235G>A		non_coding_transcript_exon	Exon 3 of 3
	ENSG00000255422	ENST00000702882.1		n.1164G>A		non_coding_transcript_exon	Exon 3 of 3
	ENSG00000255422	ENST00000526274.2	TSL:3	n.373+633G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.196 AC: 29709 AN: 151956 Hom.: 3226 Cov.: 32

Gnomad AFR AF: 0.0985

Gnomad AMI AF: 0.334

Gnomad AMR AF: 0.200

Gnomad ASJ AF: 0.195

Gnomad EAS AF: 0.223

Gnomad SAS AF: 0.297

Gnomad FIN AF: 0.238

Gnomad MID AF: 0.212

Gnomad NFE AF: 0.236

Gnomad OTH AF: 0.192

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.195 AC: 29712 AN: 152074 Hom.: 3229 Cov.: 32 AF XY: 0.198 AC XY: 14727 AN XY: 74334

African (AFR) AF: 0.0984 AC: 4082 AN: 41480

American (AMR) AF: 0.200 AC: 3060 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.195 AC: 677 AN: 3468

East Asian (EAS) AF: 0.223 AC: 1148 AN: 5158

South Asian (SAS) AF: 0.298 AC: 1439 AN: 4828

European-Finnish (FIN) AF: 0.238 AC: 2514 AN: 10574

Middle Eastern (MID) AF: 0.207 AC: 61 AN: 294

European-Non Finnish (NFE) AF: 0.236 AC: 16025 AN: 67984

Other (OTH) AF: 0.190 AC: 401 AN: 2110

Alfa AF: 0.225 Hom.: 2734

Bravo AF: 0.184

Asia WGS AF: 0.237 AC: 824 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	10
DANN	Benign	0.56
PhyloP100		0.36

Splicing

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

Other links and lift over

dbSNP: rs10892258; hg19: chr11-118579865;