chr21-17726553-C-T

Variant names:

• chr21-17726553-C-T
• rs9977139
• ENST00000813567.1:n.338+11780G>A

Variant summary

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

The ENST00000813567.1(ENSG00000226956):​n.338+11780G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.379 in 151,976 control chromosomes in the GnomAD database, including 15,603 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 0.38 (15603 hom., cov: 31)
• Consequence: ENSG00000226956 ENST00000813567.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.509
• Publications: 3 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=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.762 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000813567.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000226956	ENST00000813567.1		n.338+11780G>A		intron	N/A
	ENSG00000226956	ENST00000813568.1		n.343-10326G>A		intron	N/A
	ENSG00000244676	ENST00000813927.1		n.192-28706C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.379 AC: 57503 AN: 151858 Hom.: 15555 Cov.: 31

Gnomad AFR AF: 0.769

Gnomad AMI AF: 0.218

Gnomad AMR AF: 0.260

Gnomad ASJ AF: 0.368

Gnomad EAS AF: 0.121

Gnomad SAS AF: 0.293

Gnomad FIN AF: 0.188

Gnomad MID AF: 0.347

Gnomad NFE AF: 0.226

Gnomad OTH AF: 0.374

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

GnomAD4 genome AF: 0.379 AC: 57605 AN: 151976 Hom.: 15603 Cov.: 31 AF XY: 0.373 AC XY: 27701 AN XY: 74266

African (AFR) AF: 0.769 AC: 31884 AN: 41438

American (AMR) AF: 0.259 AC: 3959 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.368 AC: 1277 AN: 3470

East Asian (EAS) AF: 0.121 AC: 625 AN: 5150

South Asian (SAS) AF: 0.292 AC: 1404 AN: 4806

European-Finnish (FIN) AF: 0.188 AC: 1985 AN: 10566

Middle Eastern (MID) AF: 0.349 AC: 102 AN: 292

European-Non Finnish (NFE) AF: 0.226 AC: 15381 AN: 67980

Other (OTH) AF: 0.376 AC: 790 AN: 2102

Alfa AF: 0.299 Hom.: 3198

Bravo AF: 0.397

Asia WGS AF: 0.279 AC: 967 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.83
DANN	Benign	0.47
PhyloP100		-0.51

Splicing

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

Other links and lift over

dbSNP: rs9977139; hg19: chr21-19098871; COSMIC: COSV56534122;