chr11-118741072-G-A

Variant names:

• chr11-118741072-G-A
• rs10892279
• ENST00000526274.2:n.374-9141G>A

Variant summary

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

The ENST00000526274.2(ENSG00000255422):​n.374-9141G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.249 in 146,518 control chromosomes in the GnomAD database, including 4,521 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 0.25 (4521 hom., cov: 31)
• Consequence: ENSG00000255422 ENST00000526274.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.245
• Publications: 43 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=-0.87).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.381 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000526274.2. 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	ENST00000526274.2	TSL:3	n.374-9141G>A		intron	N/A
	ENSG00000308658	ENST00000835569.1		n.71-13386G>A		intron	N/A
	ENSG00000308658	ENST00000835570.1		n.500-13386G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.249 AC: 36459 AN: 146398 Hom.: 4509 Cov.: 31

Gnomad AFR AF: 0.292

Gnomad AMI AF: 0.246

Gnomad AMR AF: 0.205

Gnomad ASJ AF: 0.223

Gnomad EAS AF: 0.320

Gnomad SAS AF: 0.396

Gnomad FIN AF: 0.236

Gnomad MID AF: 0.219

Gnomad NFE AF: 0.221

Gnomad OTH AF: 0.230

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

GnomAD4 genome AF: 0.249 AC: 36496 AN: 146518 Hom.: 4521 Cov.: 31 AF XY: 0.252 AC XY: 17983 AN XY: 71440

African (AFR) AF: 0.292 AC: 11893 AN: 40708

American (AMR) AF: 0.205 AC: 3035 AN: 14826

Ashkenazi Jewish (ASJ) AF: 0.223 AC: 746 AN: 3342

East Asian (EAS) AF: 0.320 AC: 1537 AN: 4810

South Asian (SAS) AF: 0.397 AC: 1741 AN: 4386

European-Finnish (FIN) AF: 0.236 AC: 2349 AN: 9964

Middle Eastern (MID) AF: 0.218 AC: 61 AN: 280

European-Non Finnish (NFE) AF: 0.221 AC: 14468 AN: 65346

Other (OTH) AF: 0.228 AC: 456 AN: 2002

Alfa AF: 0.221 Hom.: 13793

Bravo AF: 0.234

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	1.2
DANN	Benign	0.75
PhyloP100		-0.24

Splicing

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

Other links and lift over

dbSNP: rs10892279; hg19: chr11-118611781;