rs11701130

Positions:

• chr21-45621894-G-T

Variant summary

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

The ENST00000651182.1(ENSG00000286082):​n.237+3079C>A variant causes a intron, non coding transcript 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: ENST00000651182.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.44

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000651182.1	n.237+3079C>A		intron_variant, non_coding_transcript_variant

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

Gnomad4 AFR AF: 0.165

Gnomad4 AMR AF: 0.196

Gnomad4 ASJ AF: 0.177

Gnomad4 EAS AF: 0.00443

Gnomad4 SAS AF: 0.102

Gnomad4 FIN AF: 0.265

Gnomad4 NFE AF: 0.238

Gnomad4 OTH AF: 0.188

Alfa AF: 0.223 Hom.: 6553

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11701130; hg19: chr21-47041808;