rs4872533

Positions:

• chr8-22702180-C-T

Variant summary

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

The ENST00000665743.1(ENSG00000287812):​n.1597G>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 0.486 in 151,756 control chromosomes in the GnomAD database, including 18,231 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 0.49 (18231 hom., cov: 30)
• Consequence: ENSG00000287812 ENST00000665743.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.451

Genes affected

ENSG00000287812 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.557 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.22702180C>T		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000287812	ENST00000665743.1	n.1597G>A		non_coding_transcript_exon_variant	1/2
ENSG00000253125	ENST00000523627.1	n.164+11867C>T		intron_variant		4

Frequencies

GnomAD3 genomes AF: 0.486 AC: 73705 AN: 151638 Hom.: 18211 Cov.: 30

Gnomad AFR AF: 0.547

Gnomad AMI AF: 0.646

Gnomad AMR AF: 0.566

Gnomad ASJ AF: 0.493

Gnomad EAS AF: 0.228

Gnomad SAS AF: 0.455

Gnomad FIN AF: 0.447

Gnomad MID AF: 0.522

Gnomad NFE AF: 0.456

Gnomad OTH AF: 0.496

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.486 AC: 73779 AN: 151756 Hom.: 18231 Cov.: 30 AF XY: 0.485 AC XY: 35963 AN XY: 74154

Gnomad4 AFR AF: 0.547

Gnomad4 AMR AF: 0.567

Gnomad4 ASJ AF: 0.493

Gnomad4 EAS AF: 0.229

Gnomad4 SAS AF: 0.454

Gnomad4 FIN AF: 0.447

Gnomad4 NFE AF: 0.456

Gnomad4 OTH AF: 0.497

Alfa AF: 0.465 Hom.: 18021

Bravo AF: 0.497

Asia WGS AF: 0.378 AC: 1315 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.51
DANN	Benign	0.78

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4872533; hg19: chr8-22559693;