21-37358422-T-C

Variant names:

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

Variant summary

Our verdict is Benign. Variant got -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

Genes affected

ENSG00000287637 (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 (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

Gnomad4 AFR AF: 0.682

Gnomad4 AMR AF: 0.563

Gnomad4 ASJ AF: 0.690

Gnomad4 EAS AF: 0.507

Gnomad4 SAS AF: 0.620

Gnomad4 FIN AF: 0.640

Gnomad4 NFE AF: 0.624

Gnomad4 OTH AF: 0.647

Alfa AF: 0.619 Hom.: 22256

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs8126696; hg19: chr21-38730724;