rs1002229

Variant names:

• chr11-32031461-A-T
• rs1002229
• ENST00000532942.5:c.102-65683A>T

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The ENST00000532942.5(ENSG00000285283):​c.102-65683A>T variant causes a intron change. The variant allele was found at a frequency of 0.178 in 152,124 control chromosomes in the GnomAD database, including 3,167 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 0.18 (3167 hom., cov: 32)
• Consequence: ENSG00000285283 ENST00000532942.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 4.94

Genes affected

ENSG00000285283 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.3).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.314 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
ENSG00000285283	ENST00000532942.5	c.102-65683A>T		intron_variant	Intron 1 of 5	2		ENSP00000436422.1
ENSG00000285283	ENST00000530348.5	c.-244-65683A>T		intron_variant	Intron 1 of 3	4		ENSP00000436482.1

Frequencies

GnomAD3 genomes AF: 0.178 AC: 27001 AN: 152006 Hom.: 3150 Cov.: 32

Gnomad AFR AF: 0.281

Gnomad AMI AF: 0.114

Gnomad AMR AF: 0.278

Gnomad ASJ AF: 0.127

Gnomad EAS AF: 0.327

Gnomad SAS AF: 0.296

Gnomad FIN AF: 0.0711

Gnomad MID AF: 0.178

Gnomad NFE AF: 0.0925

Gnomad OTH AF: 0.179

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

GnomAD4 genome AF: 0.178 AC: 27069 AN: 152124 Hom.: 3167 Cov.: 32 AF XY: 0.181 AC XY: 13446 AN XY: 74360

Gnomad4 AFR AF: 0.282

Gnomad4 AMR AF: 0.278

Gnomad4 ASJ AF: 0.127

Gnomad4 EAS AF: 0.327

Gnomad4 SAS AF: 0.296

Gnomad4 FIN AF: 0.0711

Gnomad4 NFE AF: 0.0925

Gnomad4 OTH AF: 0.179

Alfa AF: 0.132 Hom.: 249

Bravo AF: 0.201

Asia WGS AF: 0.273 AC: 948 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.30
CADD	Benign	21
DANN	Benign	0.88

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1002229; hg19: chr11-32053007;