chr7-22788036-A-G

Variant names:

• chr7-22788036-A-G
• rs10225286

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 0.602 in 152,092 control chromosomes in the GnomAD database, including 27,835 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 0.60 (27835 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.606
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.821 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: 0.602 AC: 91491 AN: 151974 Hom.: 27798 Cov.: 33

Gnomad AFR AF: 0.606

Gnomad AMI AF: 0.725

Gnomad AMR AF: 0.569

Gnomad ASJ AF: 0.535

Gnomad EAS AF: 0.842

Gnomad SAS AF: 0.563

Gnomad FIN AF: 0.584

Gnomad MID AF: 0.560

Gnomad NFE AF: 0.596

Gnomad OTH AF: 0.608

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

GnomAD4 genome AF: 0.602 AC: 91582 AN: 152092 Hom.: 27835 Cov.: 33 AF XY: 0.600 AC XY: 44606 AN XY: 74338

African (AFR) AF: 0.606 AC: 25114 AN: 41474

American (AMR) AF: 0.569 AC: 8693 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.535 AC: 1856 AN: 3470

East Asian (EAS) AF: 0.842 AC: 4361 AN: 5178

South Asian (SAS) AF: 0.565 AC: 2721 AN: 4816

European-Finnish (FIN) AF: 0.584 AC: 6168 AN: 10570

Middle Eastern (MID) AF: 0.568 AC: 167 AN: 294

European-Non Finnish (NFE) AF: 0.596 AC: 40542 AN: 67988

Other (OTH) AF: 0.614 AC: 1299 AN: 2116

Alfa AF: 0.602 Hom.: 8224

Bravo AF: 0.600

Asia WGS AF: 0.723 AC: 2513 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	3.2
DANN	Benign	0.59
PhyloP100		-0.61

Splicing

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

Other links and lift over

dbSNP: rs10225286; hg19: chr7-22827655;