11-76654411-C-T

Variant names:

• chr11-76654411-C-T
• rs11236836
• ENST00000531511.1:n.409G>A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000531511.1(ENSG00000254810):​n.409G>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 0.502 in 152,018 control chromosomes in the GnomAD database, including 19,444 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 0.50 (19430 hom., cov: 32)
  • Exomes 𝑓: 0.52 (14 hom.)
• Consequence: ENSG00000254810 ENST00000531511.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.551

Genes affected

ENSG00000254810 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.527 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
ENSG00000254810	ENST00000531511.1	n.409G>A		non_coding_transcript_exon_variant	Exon 2 of 2	3
ENSG00000254810	ENST00000686694.1	n.467-554G>A		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.502 AC: 76207 AN: 151810 Hom.: 19412 Cov.: 32

Gnomad AFR AF: 0.466

Gnomad AMI AF: 0.569

Gnomad AMR AF: 0.449

Gnomad ASJ AF: 0.456

Gnomad EAS AF: 0.544

Gnomad SAS AF: 0.533

Gnomad FIN AF: 0.511

Gnomad MID AF: 0.421

Gnomad NFE AF: 0.531

Gnomad OTH AF: 0.479

GnomAD4 exome AF: 0.522 AC: 47 AN: 90 Hom.: 14 Cov.: 0 AF XY: 0.517 AC XY: 30 AN XY: 58

Gnomad4 AFR exome AF: 0.667

Gnomad4 EAS exome AF: 0.750

Gnomad4 SAS exome AF: 0.750

Gnomad4 FIN exome AF: 0.583

Gnomad4 NFE exome AF: 0.442

Gnomad4 OTH exome AF: 0.583

GnomAD4 genome AF: 0.502 AC: 76262 AN: 151928 Hom.: 19430 Cov.: 32 AF XY: 0.499 AC XY: 37035 AN XY: 74228

Gnomad4 AFR AF: 0.466

Gnomad4 AMR AF: 0.449

Gnomad4 ASJ AF: 0.456

Gnomad4 EAS AF: 0.544

Gnomad4 SAS AF: 0.535

Gnomad4 FIN AF: 0.511

Gnomad4 NFE AF: 0.531

Gnomad4 OTH AF: 0.480

Alfa AF: 0.512 Hom.: 17964

Bravo AF: 0.497

Asia WGS AF: 0.550 AC: 1915 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.46
DANN	Benign	0.67

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11236836; hg19: chr11-76365455;