rs11701698

Positions:

• chr21-33021637-T-G

Variant summary

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

The variant allele was found at a frequency of 0.145 in 152,186 control chromosomes in the GnomAD database, including 2,121 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 0.14 (2121 hom., cov: 32)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.966

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.215 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.33021637T>G		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000227757	ENST00000454622.2	n.201+49267A>C		intron_variant		2

Frequencies

GnomAD3 genomes AF: 0.145 AC: 22060 AN: 152068 Hom.: 2121 Cov.: 32

Gnomad AFR AF: 0.0389

Gnomad AMI AF: 0.0439

Gnomad AMR AF: 0.126

Gnomad ASJ AF: 0.207

Gnomad EAS AF: 0.00212

Gnomad SAS AF: 0.107

Gnomad FIN AF: 0.193

Gnomad MID AF: 0.146

Gnomad NFE AF: 0.218

Gnomad OTH AF: 0.158

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

GnomAD4 genome AF: 0.145 AC: 22058 AN: 152186 Hom.: 2121 Cov.: 32 AF XY: 0.142 AC XY: 10529 AN XY: 74398

Gnomad4 AFR AF: 0.0388

Gnomad4 AMR AF: 0.125

Gnomad4 ASJ AF: 0.207

Gnomad4 EAS AF: 0.00212

Gnomad4 SAS AF: 0.107

Gnomad4 FIN AF: 0.193

Gnomad4 NFE AF: 0.218

Gnomad4 OTH AF: 0.157

Alfa AF: 0.190 Hom.: 1523

Bravo AF: 0.135

Asia WGS AF: 0.0550 AC: 190 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	0.32
DANN	Benign	0.66

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11701698; hg19: chr21-34393945;