chr21-37326857-C-T

Variant names:

• chr21-37326857-C-T
• rs11702247
• ENST00000812080.1:n.390-10471C>T

Variant summary

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

The ENST00000812080.1(ENSG00000242553):​n.390-10471C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.853 in 152,036 control chromosomes in the GnomAD database, including 55,512 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 0.85 (55512 hom., cov: 31)
• Consequence: ENSG00000242553 ENST00000812080.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.816
• Publications: 1 publications found

Genes affected

ENSG00000242553 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.97 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
ENSG00000242553	ENST00000812080.1	n.390-10471C>T		intron_variant	Intron 2 of 3

Frequencies

GnomAD3 genomes AF: 0.853 AC: 129592 AN: 151918 Hom.: 55457 Cov.: 31

Gnomad AFR AF: 0.898

Gnomad AMI AF: 0.879

Gnomad AMR AF: 0.874

Gnomad ASJ AF: 0.777

Gnomad EAS AF: 0.992

Gnomad SAS AF: 0.783

Gnomad FIN AF: 0.878

Gnomad MID AF: 0.835

Gnomad NFE AF: 0.816

Gnomad OTH AF: 0.834

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

GnomAD4 genome AF: 0.853 AC: 129710 AN: 152036 Hom.: 55512 Cov.: 31 AF XY: 0.854 AC XY: 63476 AN XY: 74342

African (AFR) AF: 0.898 AC: 37261 AN: 41482

American (AMR) AF: 0.874 AC: 13348 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.777 AC: 2696 AN: 3468

East Asian (EAS) AF: 0.992 AC: 5142 AN: 5182

South Asian (SAS) AF: 0.784 AC: 3771 AN: 4812

European-Finnish (FIN) AF: 0.878 AC: 9246 AN: 10534

Middle Eastern (MID) AF: 0.837 AC: 246 AN: 294

European-Non Finnish (NFE) AF: 0.816 AC: 55438 AN: 67976

Other (OTH) AF: 0.836 AC: 1764 AN: 2110

Alfa AF: 0.842 Hom.: 30799

Bravo AF: 0.858

Asia WGS AF: 0.908 AC: 3138 AN: 3458

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.62
DANN	Benign	0.48
PhyloP100		-0.82

Splicing

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

Other links and lift over

dbSNP: rs11702247; hg19: chr21-38699159;