11-76654411-C-T

Position:

• chr11-76654411-C-T

Variant summary

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

The ENST00000686694.1(ENSG00000254810):​n.467-554G>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 0.502 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: ENST00000686694.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.551

Genes affected

(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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000686694.1	n.467-554G>A		intron_variant, non_coding_transcript_variant
	ENST00000531511.1	n.409G>A		non_coding_transcript_exon_variant	2/2	3

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;