rs1002229

Positions:

• chr11-32031461-A-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/exons	MANE	Protein	UniProt
		n.32031461A>T		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000285283	ENST00000532942.5	c.102-65683A>T		intron_variant		2		ENSP00000436422.1
ENSG00000285283	ENST00000530348.5	c.-244-65683A>T		intron_variant		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;