rs11701130

Variant names:

• chr21-45621894-G-T
• rs11701130
• ENST00000651182.1:n.237+3079C>A

Variant summary

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

The ENST00000651182.1(ENSG00000286082):​n.237+3079C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.202 in 152,148 control chromosomes in the GnomAD database, including 3,370 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 (3370 hom., cov: 33)
• Consequence: ENSG00000286082 ENST00000651182.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.44
• Publications: 7 publications found

Genes affected

ENSG00000286082 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.235 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
ENSG00000286082	ENST00000651182.1	n.237+3079C>A		intron_variant	Intron 2 of 3

Frequencies

GnomAD3 genomes AF: 0.202 AC: 30659 AN: 152030 Hom.: 3369 Cov.: 33

Gnomad AFR AF: 0.165

Gnomad AMI AF: 0.320

Gnomad AMR AF: 0.196

Gnomad ASJ AF: 0.177

Gnomad EAS AF: 0.00442

Gnomad SAS AF: 0.101

Gnomad FIN AF: 0.265

Gnomad MID AF: 0.108

Gnomad NFE AF: 0.238

Gnomad OTH AF: 0.190

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

GnomAD4 genome AF: 0.202 AC: 30683 AN: 152148 Hom.: 3370 Cov.: 33 AF XY: 0.201 AC XY: 14948 AN XY: 74378

African (AFR) AF: 0.165 AC: 6862 AN: 41524

American (AMR) AF: 0.196 AC: 2999 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.177 AC: 615 AN: 3470

East Asian (EAS) AF: 0.00443 AC: 23 AN: 5192

South Asian (SAS) AF: 0.102 AC: 493 AN: 4828

European-Finnish (FIN) AF: 0.265 AC: 2807 AN: 10574

Middle Eastern (MID) AF: 0.120 AC: 35 AN: 292

European-Non Finnish (NFE) AF: 0.238 AC: 16161 AN: 67966

Other (OTH) AF: 0.188 AC: 396 AN: 2108

Alfa AF: 0.220 Hom.: 9844

Bravo AF: 0.196

Asia WGS AF: 0.0480 AC: 167 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.35
DANN	Benign	0.48
PhyloP100		-1.4

Splicing

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

Other links and lift over

dbSNP: rs11701130; hg19: chr21-47041808;