rs11583328

Variant names:

• chr1-201033045-G-A
• rs11583328
• ENST00000610411.1:n.96+1814G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000610411.1(ENSG00000234132):​n.96+1814G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.195 in 152,178 control chromosomes in the GnomAD database, including 3,619 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 0.20 (3619 hom., cov: 32)
• Consequence: ENSG00000234132 ENST00000610411.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.115
• Publications: 9 publications found

Genes affected

ENSG00000234132 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.281 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC101929305	NR_188461.1	n.1229+1680G>A		intron_variant	Intron 3 of 4
LOC101929305	NR_188462.1	n.989+1814G>A		intron_variant	Intron 3 of 4
LOC101929305	NR_188463.1	n.245-2007G>A		intron_variant	Intron 2 of 3
LOC101929305	NR_188464.1	n.254-2007G>A		intron_variant	Intron 2 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000234132	ENST00000610411.1	n.96+1814G>A		intron_variant	Intron 1 of 2	4
ENSG00000234132	ENST00000738484.1	n.253+7426G>A		intron_variant	Intron 2 of 3
ENSG00000234132	ENST00000738485.1	n.325-2007G>A		intron_variant	Intron 2 of 3

Frequencies

GnomAD3 genomes AF: 0.195 AC: 29676 AN: 152060 Hom.: 3618 Cov.: 32

Gnomad AFR AF: 0.0887

Gnomad AMI AF: 0.439

Gnomad AMR AF: 0.153

Gnomad ASJ AF: 0.225

Gnomad EAS AF: 0.00558

Gnomad SAS AF: 0.101

Gnomad FIN AF: 0.204

Gnomad MID AF: 0.253

Gnomad NFE AF: 0.284

Gnomad OTH AF: 0.198

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

GnomAD4 genome AF: 0.195 AC: 29676 AN: 152178 Hom.: 3619 Cov.: 32 AF XY: 0.189 AC XY: 14038 AN XY: 74408

African (AFR) AF: 0.0887 AC: 3685 AN: 41534

American (AMR) AF: 0.152 AC: 2328 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.225 AC: 782 AN: 3472

East Asian (EAS) AF: 0.00559 AC: 29 AN: 5184

South Asian (SAS) AF: 0.102 AC: 490 AN: 4820

European-Finnish (FIN) AF: 0.204 AC: 2157 AN: 10582

Middle Eastern (MID) AF: 0.245 AC: 72 AN: 294

European-Non Finnish (NFE) AF: 0.284 AC: 19320 AN: 67988

Other (OTH) AF: 0.196 AC: 413 AN: 2112

Alfa AF: 0.225 Hom.: 1172

Bravo AF: 0.187

Asia WGS AF: 0.0630 AC: 221 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	2.0
DANN	Benign	0.78
PhyloP100		0.12

Splicing

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

Other links and lift over

dbSNP: rs11583328; hg19: chr1-201002173;