rs8126696

Positions:

• chr21-37358422-T-C
• chr21-37358422-T-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

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: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.24

Genes affected

(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/exons	MANE	Protein	UniProt
		n.37358422T>C		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000287637	ENST00000663813.1	n.187+8250A>G		intron_variant

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;