rs2079069

Positions:

• chr7-84604517-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 0.0297 in 152,228 control chromosomes in the GnomAD database, including 161 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 0.030 (161 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.347

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 (EAS) allele frequency at 95% confidence interval = 0.146 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.0297 AC: 4519 AN: 152110 Hom.: 161 Cov.: 32

Gnomad AFR AF: 0.0580

Gnomad AMI AF: 0.00329

Gnomad AMR AF: 0.0472

Gnomad ASJ AF: 0.0202

Gnomad EAS AF: 0.155

Gnomad SAS AF: 0.0114

Gnomad FIN AF: 0.00989

Gnomad MID AF: 0.00633

Gnomad NFE AF: 0.00444

Gnomad OTH AF: 0.0268

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

GnomAD4 genome AF: 0.0297 AC: 4520 AN: 152228 Hom.: 161 Cov.: 32 AF XY: 0.0302 AC XY: 2251 AN XY: 74418

Gnomad4 AFR AF: 0.0580

Gnomad4 AMR AF: 0.0471

Gnomad4 ASJ AF: 0.0202

Gnomad4 EAS AF: 0.155

Gnomad4 SAS AF: 0.0112

Gnomad4 FIN AF: 0.00989

Gnomad4 NFE AF: 0.00444

Gnomad4 OTH AF: 0.0260

Alfa AF: 0.0237 Hom.: 16

Bravo AF: 0.0352

Asia WGS AF: 0.0770 AC: 266 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	3.7
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: rs2079069; hg19: chr7-84233833;