7-80970041-A-G

Position:

• chr7-80970041-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 0.674 in 151,890 control chromosomes in the GnomAD database, including 35,589 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 0.67 (35589 hom., cov: 30)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.961

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.763 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.80970041A>G		intergenic_region

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.675 AC: 102380 AN: 151772 Hom.: 35563 Cov.: 30

Gnomad AFR AF: 0.499

Gnomad AMI AF: 0.806

Gnomad AMR AF: 0.774

Gnomad ASJ AF: 0.733

Gnomad EAS AF: 0.578

Gnomad SAS AF: 0.726

Gnomad FIN AF: 0.736

Gnomad MID AF: 0.669

Gnomad NFE AF: 0.747

Gnomad OTH AF: 0.695

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

GnomAD4 genome AF: 0.674 AC: 102449 AN: 151890 Hom.: 35589 Cov.: 30 AF XY: 0.674 AC XY: 50033 AN XY: 74234

Gnomad4 AFR AF: 0.499

Gnomad4 AMR AF: 0.774

Gnomad4 ASJ AF: 0.733

Gnomad4 EAS AF: 0.579

Gnomad4 SAS AF: 0.727

Gnomad4 FIN AF: 0.736

Gnomad4 NFE AF: 0.747

Gnomad4 OTH AF: 0.694

Alfa AF: 0.734 Hom.: 92177

Bravo AF: 0.667

Asia WGS AF: 0.659 AC: 2289 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.57
DANN	Benign	0.75

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4236644; hg19: chr7-80599357;