chr7-128115900-A-G

Variant names:

• chr7-128115900-A-G
• rs322785

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 0.505 in 152,094 control chromosomes in the GnomAD database, including 20,259 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 0.51 (20259 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.584

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 (AFR) allele frequency at 95% confidence interval = 0.642 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: 0.505 AC: 76782 AN: 151976 Hom.: 20248 Cov.: 33

Gnomad AFR AF: 0.649

Gnomad AMI AF: 0.594

Gnomad AMR AF: 0.498

Gnomad ASJ AF: 0.498

Gnomad EAS AF: 0.158

Gnomad SAS AF: 0.362

Gnomad FIN AF: 0.408

Gnomad MID AF: 0.462

Gnomad NFE AF: 0.471

Gnomad OTH AF: 0.482

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

GnomAD4 genome AF: 0.505 AC: 76831 AN: 152094 Hom.: 20259 Cov.: 33 AF XY: 0.495 AC XY: 36816 AN XY: 74352

Gnomad4 AFR AF: 0.648

Gnomad4 AMR AF: 0.498

Gnomad4 ASJ AF: 0.498

Gnomad4 EAS AF: 0.159

Gnomad4 SAS AF: 0.360

Gnomad4 FIN AF: 0.408

Gnomad4 NFE AF: 0.471

Gnomad4 OTH AF: 0.480

Alfa AF: 0.496 Hom.: 2393

Bravo AF: 0.521

Asia WGS AF: 0.284 AC: 995 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	3.0
DANN	Benign	0.69

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs322785; hg19: chr7-127755952; COSMIC: COSV53500497;