chr21-17667969-C-A

Variant names:

• chr21-17667969-C-A
• rs10482889
• ENST00000416641.2:n.210+7081G>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000416641.2(ENSG00000226956):​n.210+7081G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0934 in 152,152 control chromosomes in the GnomAD database, including 1,888 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 0.093 (1888 hom., cov: 32)
• Consequence: ENSG00000226956 ENST00000416641.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.128
• Publications: 1 publications found

Genes affected

ENSG00000226956 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.285 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000416641.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000226956	ENST00000416641.2	TSL:3	n.210+7081G>T		intron	N/A
	ENSG00000226956	ENST00000813567.1		n.339-8300G>T		intron	N/A
	ENSG00000226956	ENST00000813569.1		n.222+7081G>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0933 AC: 14179 AN: 152034 Hom.: 1881 Cov.: 32

Gnomad AFR AF: 0.289

Gnomad AMI AF: 0.0735

Gnomad AMR AF: 0.0485

Gnomad ASJ AF: 0.0769

Gnomad EAS AF: 0.0248

Gnomad SAS AF: 0.0678

Gnomad FIN AF: 0.00302

Gnomad MID AF: 0.0601

Gnomad NFE AF: 0.00738

Gnomad OTH AF: 0.0708

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

GnomAD4 genome AF: 0.0934 AC: 14211 AN: 152152 Hom.: 1888 Cov.: 32 AF XY: 0.0918 AC XY: 6831 AN XY: 74414

African (AFR) AF: 0.289 AC: 11975 AN: 41454

American (AMR) AF: 0.0483 AC: 739 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.0769 AC: 267 AN: 3470

East Asian (EAS) AF: 0.0249 AC: 129 AN: 5184

South Asian (SAS) AF: 0.0666 AC: 321 AN: 4818

European-Finnish (FIN) AF: 0.00302 AC: 32 AN: 10608

Middle Eastern (MID) AF: 0.0612 AC: 18 AN: 294

European-Non Finnish (NFE) AF: 0.00737 AC: 501 AN: 68008

Other (OTH) AF: 0.0767 AC: 162 AN: 2112

Alfa AF: 0.0329 Hom.: 255

Bravo AF: 0.105

Asia WGS AF: 0.0690 AC: 240 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	1.5
DANN	Benign	0.73
PhyloP100		0.13

Splicing

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

Other links and lift over

dbSNP: rs10482889; hg19: chr21-19040287;