rs881666

Positions:

• chr21-33032958-C-G

Variant summary

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

The ENST00000454622.2(ENSG00000227757):​n.201+37946G>C 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 0.319 in 152,028 control chromosomes in the GnomAD database, including 8,821 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 0.32 (8821 hom., cov: 32)
• Consequence: ENST00000454622.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.817

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.413 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
	ENST00000454622.2	n.201+37946G>C		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.319 AC: 48421 AN: 151910 Hom.: 8820 Cov.: 32

Gnomad AFR AF: 0.196

Gnomad AMI AF: 0.168

Gnomad AMR AF: 0.272

Gnomad ASJ AF: 0.425

Gnomad EAS AF: 0.00443

Gnomad SAS AF: 0.232

Gnomad FIN AF: 0.400

Gnomad MID AF: 0.339

Gnomad NFE AF: 0.417

Gnomad OTH AF: 0.350

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

GnomAD4 genome AF: 0.319 AC: 48440 AN: 152028 Hom.: 8821 Cov.: 32 AF XY: 0.315 AC XY: 23371 AN XY: 74310

Gnomad4 AFR AF: 0.196

Gnomad4 AMR AF: 0.271

Gnomad4 ASJ AF: 0.425

Gnomad4 EAS AF: 0.00444

Gnomad4 SAS AF: 0.232

Gnomad4 FIN AF: 0.400

Gnomad4 NFE AF: 0.417

Gnomad4 OTH AF: 0.346

Alfa AF: 0.361 Hom.: 1333

Bravo AF: 0.305

Asia WGS AF: 0.117 AC: 407 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.68
DANN	Benign	0.47

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs881666; hg19: chr21-34405266;