21-33029641-G-C

Variant names:

• chr21-33029641-G-C
• rs9653711
• ENST00000454622.2:n.201+41263C>G

Variant summary

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

The ENST00000454622.2(ENSG00000227757):​n.201+41263C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.414 in 152,112 control chromosomes in the GnomAD database, including 15,431 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 0.41 (15431 hom., cov: 33)
• Consequence: ENSG00000227757 ENST00000454622.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.07

Genes affected

ENSG00000227757 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.548 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+41263C>G		intron_variant	Intron 1 of 1	2

Frequencies

GnomAD3 genomes AF: 0.415 AC: 63029 AN: 151994 Hom.: 15429 Cov.: 33

Gnomad AFR AF: 0.159

Gnomad AMI AF: 0.287

Gnomad AMR AF: 0.447

Gnomad ASJ AF: 0.642

Gnomad EAS AF: 0.168

Gnomad SAS AF: 0.437

Gnomad FIN AF: 0.520

Gnomad MID AF: 0.443

Gnomad NFE AF: 0.553

Gnomad OTH AF: 0.452

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

GnomAD4 genome AF: 0.414 AC: 63036 AN: 152112 Hom.: 15431 Cov.: 33 AF XY: 0.413 AC XY: 30732 AN XY: 74358

Gnomad4 AFR AF: 0.159

Gnomad4 AMR AF: 0.447

Gnomad4 ASJ AF: 0.642

Gnomad4 EAS AF: 0.168

Gnomad4 SAS AF: 0.439

Gnomad4 FIN AF: 0.520

Gnomad4 NFE AF: 0.553

Gnomad4 OTH AF: 0.447

Alfa AF: 0.335 Hom.: 980

Bravo AF: 0.400

Asia WGS AF: 0.268 AC: 931 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.029
DANN	Benign	0.49

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9653711; hg19: chr21-34401949; COSMIC: COSV60973281;