rs10892279

chr11-118741072-G-Achr11-118741072-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, non coding transcript 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: ENST00000526274.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.245

Genes affected

(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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000526274.2	n.374-9141G>A		intron_variant, non_coding_transcript_variant		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;