1-37078622-A-G

Position:

• chr1-37078622-A-G

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 0.811 in 152,132 control chromosomes in the GnomAD database, including 50,774 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 0.81 (50774 hom., cov: 31)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.75

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.54).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.899 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.37078622A>G		intergenic_region

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.811 AC: 123258 AN: 152016 Hom.: 50719 Cov.: 31

Gnomad AFR AF: 0.906

Gnomad AMI AF: 0.720

Gnomad AMR AF: 0.848

Gnomad ASJ AF: 0.824

Gnomad EAS AF: 0.407

Gnomad SAS AF: 0.751

Gnomad FIN AF: 0.743

Gnomad MID AF: 0.791

Gnomad NFE AF: 0.790

Gnomad OTH AF: 0.828

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

GnomAD4 genome AF: 0.811 AC: 123373 AN: 152132 Hom.: 50774 Cov.: 31 AF XY: 0.805 AC XY: 59865 AN XY: 74386

Gnomad4 AFR AF: 0.906

Gnomad4 AMR AF: 0.848

Gnomad4 ASJ AF: 0.824

Gnomad4 EAS AF: 0.407

Gnomad4 SAS AF: 0.752

Gnomad4 FIN AF: 0.743

Gnomad4 NFE AF: 0.790

Gnomad4 OTH AF: 0.825

Alfa AF: 0.801 Hom.: 73731

Bravo AF: 0.821

Asia WGS AF: 0.634 AC: 2205 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.54
CADD	Benign	17
DANN	Benign	0.68

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs218428; hg19: chr1-37544223;