rs1820453

Variant names:

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

Your query was ambiguous. Multiple possible variants found:

• chr11-102109604-C-A
• chr11-102109604-C-G
• chr11-102109604-C-T

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 20 publications found

Genes affected

ENSG00000260008 (HGNC:):

ENSG00000277459 (HGNC:58148):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000566440.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	YAP1-DT	NR_198976.1		n.*223G>T		downstream_gene	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000260008	ENST00000566440.1	TSL:6	n.1719C>A		non_coding_transcript_exon	Exon 1 of 1
	ENSG00000277459	ENST00000614441.1	TSL:6	n.*223G>T		downstream_gene	N/A

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

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AF: 0.500 AC: 2 AN: 4

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.500 AC: 1 AN: 2

Other (OTH) AC: 0 AN: 0

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

African (AFR) AF: 0.665 AC: 27574 AN: 41448

American (AMR) AF: 0.601 AC: 9179 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.416 AC: 1444 AN: 3468

East Asian (EAS) AF: 0.740 AC: 3835 AN: 5180

South Asian (SAS) AF: 0.437 AC: 2104 AN: 4820

European-Finnish (FIN) AF: 0.481 AC: 5072 AN: 10536

Middle Eastern (MID) AF: 0.425 AC: 125 AN: 294

European-Non Finnish (NFE) AF: 0.463 AC: 31477 AN: 67936

Other (OTH) AF: 0.530 AC: 1115 AN: 2104

Alfa AF: 0.491 Hom.: 63622

Bravo AF: 0.563

Asia WGS AF: 0.581 AC: 2022 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.73
CADD	Benign	2.1
DANN	Benign	0.87
PhyloP100		0.0070

Splicing

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

Other links and lift over

dbSNP: rs1820453; hg19: chr11-101980335;