chr7-86530517-A-G

Variant names:

• chr7-86530517-A-G
• rs2456846

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.363 in 151,938 control chromosomes in the GnomAD database, including 10,768 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 0.36 (10768 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.153
• Publications: 0 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.67).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.581 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.363 AC: 55136 AN: 151818 Hom.: 10734 Cov.: 32

Gnomad AFR AF: 0.451

Gnomad AMI AF: 0.465

Gnomad AMR AF: 0.430

Gnomad ASJ AF: 0.338

Gnomad EAS AF: 0.599

Gnomad SAS AF: 0.473

Gnomad FIN AF: 0.284

Gnomad MID AF: 0.329

Gnomad NFE AF: 0.282

Gnomad OTH AF: 0.340

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

GnomAD4 genome AF: 0.363 AC: 55219 AN: 151938 Hom.: 10768 Cov.: 32 AF XY: 0.369 AC XY: 27388 AN XY: 74272

African (AFR) AF: 0.451 AC: 18706 AN: 41432

American (AMR) AF: 0.431 AC: 6574 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.338 AC: 1172 AN: 3468

East Asian (EAS) AF: 0.598 AC: 3093 AN: 5170

South Asian (SAS) AF: 0.472 AC: 2277 AN: 4822

European-Finnish (FIN) AF: 0.284 AC: 2997 AN: 10566

Middle Eastern (MID) AF: 0.327 AC: 96 AN: 294

European-Non Finnish (NFE) AF: 0.282 AC: 19153 AN: 67900

Other (OTH) AF: 0.345 AC: 727 AN: 2110

Alfa AF: 0.307 Hom.: 911

Bravo AF: 0.376

Asia WGS AF: 0.507 AC: 1763 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.67
CADD	Benign	9.1
DANN	Benign	0.97
PhyloP100		0.15

Splicing

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

Other links and lift over

dbSNP: rs2456846; hg19: chr7-86159833;