7-83878225-A-G

Variant names:

• chr7-83878225-A-G
• rs1524332

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 0.176 in 150,784 control chromosomes in the GnomAD database, including 3,518 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 0.18 (3518 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.186
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.367 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: 0.176 AC: 26471 AN: 150666 Hom.: 3503 Cov.: 30

Gnomad AFR AF: 0.371

Gnomad AMI AF: 0.158

Gnomad AMR AF: 0.130

Gnomad ASJ AF: 0.0909

Gnomad EAS AF: 0.0536

Gnomad SAS AF: 0.0570

Gnomad FIN AF: 0.0568

Gnomad MID AF: 0.104

Gnomad NFE AF: 0.108

Gnomad OTH AF: 0.185

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

GnomAD4 genome AF: 0.176 AC: 26526 AN: 150784 Hom.: 3518 Cov.: 30 AF XY: 0.170 AC XY: 12529 AN XY: 73650

African (AFR) AF: 0.372 AC: 15266 AN: 41068

American (AMR) AF: 0.129 AC: 1938 AN: 14984

Ashkenazi Jewish (ASJ) AF: 0.0909 AC: 315 AN: 3466

East Asian (EAS) AF: 0.0538 AC: 275 AN: 5116

South Asian (SAS) AF: 0.0564 AC: 268 AN: 4754

European-Finnish (FIN) AF: 0.0568 AC: 591 AN: 10412

Middle Eastern (MID) AF: 0.109 AC: 32 AN: 294

European-Non Finnish (NFE) AF: 0.108 AC: 7316 AN: 67702

Other (OTH) AF: 0.184 AC: 381 AN: 2076

Alfa AF: 0.125 Hom.: 2439

Bravo AF: 0.191

Asia WGS AF: 0.0910 AC: 315 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.36
DANN	Benign	0.63
PhyloP100		-0.19

Splicing

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

Other links and lift over

dbSNP: rs1524332; hg19: chr7-83507541;