8-40044278-A-G

Position:

• chr8-40044278-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 0.91 in 152,272 control chromosomes in the GnomAD database, including 63,180 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 0.91 (63180 hom., cov: 33)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.611

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.971 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.40044278A>G		intergenic_region

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.910 AC: 138458 AN: 152154 Hom.: 63134 Cov.: 33

Gnomad AFR AF: 0.920

Gnomad AMI AF: 0.944

Gnomad AMR AF: 0.830

Gnomad ASJ AF: 0.943

Gnomad EAS AF: 0.994

Gnomad SAS AF: 0.980

Gnomad FIN AF: 0.902

Gnomad MID AF: 0.972

Gnomad NFE AF: 0.909

Gnomad OTH AF: 0.912

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

GnomAD4 genome AF: 0.910 AC: 138558 AN: 152272 Hom.: 63180 Cov.: 33 AF XY: 0.911 AC XY: 67807 AN XY: 74436

Gnomad4 AFR AF: 0.920

Gnomad4 AMR AF: 0.829

Gnomad4 ASJ AF: 0.943

Gnomad4 EAS AF: 0.994

Gnomad4 SAS AF: 0.980

Gnomad4 FIN AF: 0.902

Gnomad4 NFE AF: 0.909

Gnomad4 OTH AF: 0.912

Alfa AF: 0.893 Hom.: 9584

Bravo AF: 0.899

Asia WGS AF: 0.979 AC: 3405 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	1.1
DANN	Benign	0.36

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2929115; hg19: chr8-39901797;