chr11-102109604-C-A

Variant names:

• chr11-102109604-C-A
• rs1820453
• ENST00000566440.1:n.1719C>A

Variant summary

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

The ENST00000566440.1(ENSG00000260008):​n.1719C>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 0.542 in 151,966 control chromosomes in the GnomAD database, including 23,067 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 0.54 (23066 hom., cov: 32)
  • Exomes 𝑓: 0.50 (1 hom.)
• Consequence: ENSG00000260008 ENST00000566440.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.00700

Genes affected

ENSG00000260008 (HGNC:):

ENSG00000277459 (HGNC:58148):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.73).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.721 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
ENSG00000260008	ENST00000566440.1	n.1719C>A		non_coding_transcript_exon_variant	Exon 1 of 1	6
ENSG00000277459	ENST00000614441.1	n.*223G>T		downstream_gene_variant		6

Frequencies

GnomAD3 genomes AF: 0.542 AC: 82232 AN: 151842 Hom.: 23028 Cov.: 32

Gnomad AFR AF: 0.665

Gnomad AMI AF: 0.434

Gnomad AMR AF: 0.602

Gnomad ASJ AF: 0.416

Gnomad EAS AF: 0.740

Gnomad SAS AF: 0.436

Gnomad FIN AF: 0.481

Gnomad MID AF: 0.424

Gnomad NFE AF: 0.463

Gnomad OTH AF: 0.536

GnomAD4 exome AF: 0.500 AC: 3 AN: 6 Hom.: 1 Cov.: 0 AF XY: 0.500 AC XY: 2 AN XY: 4

Gnomad4 FIN exome AF: 0.500

Gnomad4 NFE exome AF: 0.500

GnomAD4 genome AF: 0.542 AC: 82320 AN: 151960 Hom.: 23066 Cov.: 32 AF XY: 0.543 AC XY: 40356 AN XY: 74294

Gnomad4 AFR AF: 0.665

Gnomad4 AMR AF: 0.601

Gnomad4 ASJ AF: 0.416

Gnomad4 EAS AF: 0.740

Gnomad4 SAS AF: 0.437

Gnomad4 FIN AF: 0.481

Gnomad4 NFE AF: 0.463

Gnomad4 OTH AF: 0.530

Alfa AF: 0.479 Hom.: 21371

Bravo AF: 0.563

Asia WGS AF: 0.581 AC: 2022 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.73
CADD	Benign	2.1
DANN	Benign	0.87

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1820453; hg19: chr11-101980335;