21-38675252-G-A

Position:

• chr21-38675252-G-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 0.747 in 150,954 control chromosomes in the GnomAD database, including 42,197 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 0.75 (42197 hom., cov: 26)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.100

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.771 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.38675252G>A		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.747 AC: 112713 AN: 150838 Hom.: 42146 Cov.: 26

Gnomad AFR AF: 0.719

Gnomad AMI AF: 0.879

Gnomad AMR AF: 0.745

Gnomad ASJ AF: 0.824

Gnomad EAS AF: 0.739

Gnomad SAS AF: 0.790

Gnomad FIN AF: 0.729

Gnomad MID AF: 0.774

Gnomad NFE AF: 0.760

Gnomad OTH AF: 0.731

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

GnomAD4 genome AF: 0.747 AC: 112816 AN: 150954 Hom.: 42197 Cov.: 26 AF XY: 0.748 AC XY: 55128 AN XY: 73712

Gnomad4 AFR AF: 0.720

Gnomad4 AMR AF: 0.745

Gnomad4 ASJ AF: 0.824

Gnomad4 EAS AF: 0.739

Gnomad4 SAS AF: 0.792

Gnomad4 FIN AF: 0.729

Gnomad4 NFE AF: 0.760

Gnomad4 OTH AF: 0.732

Alfa AF: 0.758 Hom.: 19375

Bravo AF: 0.747

Asia WGS AF: 0.752 AC: 2614 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	5.7
DANN	Benign	0.71

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2836613; hg19: chr21-40047176;