chr21-37358422-T-C

Variant names:

• chr21-37358422-T-C
• rs8126696
• ENST00000663813.1:n.187+8250A>G

Variant summary

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

The ENST00000663813.1(ENSG00000287637):​n.187+8250A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.633 in 151,962 control chromosomes in the GnomAD database, including 30,646 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 0.63 (30646 hom., cov: 31)
• Consequence: ENSG00000287637 ENST00000663813.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.24
• Publications: 10 publications found

Genes affected

ENSG00000287637 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.675 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
ENSG00000287637	ENST00000663813.1	n.187+8250A>G		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.632 AC: 96037 AN: 151844 Hom.: 30612 Cov.: 31

Gnomad AFR AF: 0.682

Gnomad AMI AF: 0.575

Gnomad AMR AF: 0.563

Gnomad ASJ AF: 0.690

Gnomad EAS AF: 0.509

Gnomad SAS AF: 0.619

Gnomad FIN AF: 0.640

Gnomad MID AF: 0.680

Gnomad NFE AF: 0.624

Gnomad OTH AF: 0.645

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

GnomAD4 genome AF: 0.633 AC: 96124 AN: 151962 Hom.: 30646 Cov.: 31 AF XY: 0.629 AC XY: 46699 AN XY: 74282

African (AFR) AF: 0.682 AC: 28284 AN: 41470

American (AMR) AF: 0.563 AC: 8592 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.690 AC: 2393 AN: 3468

East Asian (EAS) AF: 0.507 AC: 2609 AN: 5146

South Asian (SAS) AF: 0.620 AC: 2990 AN: 4822

European-Finnish (FIN) AF: 0.640 AC: 6761 AN: 10556

Middle Eastern (MID) AF: 0.670 AC: 197 AN: 294

European-Non Finnish (NFE) AF: 0.624 AC: 42412 AN: 67924

Other (OTH) AF: 0.647 AC: 1363 AN: 2108

Alfa AF: 0.623 Hom.: 30614

Bravo AF: 0.629

Asia WGS AF: 0.578 AC: 2011 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	0.83
DANN	Benign	0.47
PhyloP100		-1.2

Splicing

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

Other links and lift over

dbSNP: rs8126696; hg19: chr21-38730724;