chr7-107812658-G-A

Variant names:

• chr7-107812658-G-A
• rs2108225

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 0.549 in 151,520 control chromosomes in the GnomAD database, including 24,937 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 0.55 (24937 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.527
• Publications: 26 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.796 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: 0.549 AC: 83149 AN: 151412 Hom.: 24889 Cov.: 30

Gnomad AFR AF: 0.803

Gnomad AMI AF: 0.333

Gnomad AMR AF: 0.487

Gnomad ASJ AF: 0.405

Gnomad EAS AF: 0.400

Gnomad SAS AF: 0.532

Gnomad FIN AF: 0.506

Gnomad MID AF: 0.462

Gnomad NFE AF: 0.439

Gnomad OTH AF: 0.534

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

GnomAD4 genome AF: 0.549 AC: 83259 AN: 151520 Hom.: 24937 Cov.: 30 AF XY: 0.548 AC XY: 40584 AN XY: 74010

African (AFR) AF: 0.803 AC: 33225 AN: 41360

American (AMR) AF: 0.488 AC: 7420 AN: 15218

Ashkenazi Jewish (ASJ) AF: 0.405 AC: 1406 AN: 3468

East Asian (EAS) AF: 0.400 AC: 2065 AN: 5158

South Asian (SAS) AF: 0.533 AC: 2563 AN: 4806

European-Finnish (FIN) AF: 0.506 AC: 5236 AN: 10338

Middle Eastern (MID) AF: 0.459 AC: 134 AN: 292

European-Non Finnish (NFE) AF: 0.439 AC: 29790 AN: 67872

Other (OTH) AF: 0.532 AC: 1118 AN: 2102

Alfa AF: 0.465 Hom.: 79142

Bravo AF: 0.560

Asia WGS AF: 0.499 AC: 1727 AN: 3466

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	5.9
DANN	Benign	0.44
PhyloP100		0.53

Splicing

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

Other links and lift over

dbSNP: rs2108225; hg19: chr7-107453103;