rs11701698

Variant names:

• chr21-33021637-T-G
• rs11701698
• ENST00000454622.2:n.201+49267A>C

Variant summary

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

The ENST00000454622.2(ENSG00000227757):​n.201+49267A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. 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: ENSG00000227757 ENST00000454622.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.966

Genes affected

ENSG00000227757 (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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000227757	ENST00000454622.2	n.201+49267A>C		intron_variant	Intron 1 of 1	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;