rs10892279

Variant names:

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

Your query was ambiguous. Multiple possible variants found:

• chr11-118741072-G-A
• chr11-118741072-G-T

Variant summary

Our verdict is Benign. Variant got -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

Genes affected

ENSG00000255422 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

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
ENSG00000255422	ENST00000526274.2	n.374-9141G>A		intron_variant	Intron 2 of 2	3

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

Gnomad4 AFR AF: 0.292

Gnomad4 AMR AF: 0.205

Gnomad4 ASJ AF: 0.223

Gnomad4 EAS AF: 0.320

Gnomad4 SAS AF: 0.397

Gnomad4 FIN AF: 0.236

Gnomad4 NFE AF: 0.221

Gnomad4 OTH AF: 0.228

Alfa AF: 0.219 Hom.: 6391

Bravo AF: 0.234

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10892279; hg19: chr11-118611781;