rs1769813

Variant names:

• chr1-231445839-A-T
• rs1769813
• ENST00000662216.1:c.30+16599T>A

Variant summary

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

The ENST00000662216.1(ENSG00000287856):​c.30+16599T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.321 in 151,798 control chromosomes in the GnomAD database, including 9,238 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 0.32 (9238 hom., cov: 30)
• Consequence: ENSG00000287856 ENST00000662216.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.11

Genes affected

ENSG00000287856 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.506 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
ENSG00000287856	ENST00000662216.1	c.30+16599T>A		intron_variant	Intron 3 of 6			ENSP00000499467.1
ENSG00000287856	ENST00000653908.1	c.30+16599T>A		intron_variant	Intron 2 of 4			ENSP00000499669.1
ENSG00000287856	ENST00000653198.1	n.433+16633T>A		intron_variant	Intron 4 of 7

Frequencies

GnomAD3 genomes AF: 0.321 AC: 48700 AN: 151680 Hom.: 9207 Cov.: 30

Gnomad AFR AF: 0.511

Gnomad AMI AF: 0.280

Gnomad AMR AF: 0.337

Gnomad ASJ AF: 0.230

Gnomad EAS AF: 0.0369

Gnomad SAS AF: 0.120

Gnomad FIN AF: 0.183

Gnomad MID AF: 0.245

Gnomad NFE AF: 0.266

Gnomad OTH AF: 0.294

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

GnomAD4 genome AF: 0.321 AC: 48779 AN: 151798 Hom.: 9238 Cov.: 30 AF XY: 0.310 AC XY: 23012 AN XY: 74172

Gnomad4 AFR AF: 0.511

Gnomad4 AMR AF: 0.337

Gnomad4 ASJ AF: 0.230

Gnomad4 EAS AF: 0.0367

Gnomad4 SAS AF: 0.121

Gnomad4 FIN AF: 0.183

Gnomad4 NFE AF: 0.266

Gnomad4 OTH AF: 0.292

Alfa AF: 0.296 Hom.: 911

Bravo AF: 0.347

Asia WGS AF: 0.113 AC: 398 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	1.0
DANN	Benign	0.58

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1769813; hg19: chr1-231581585;