rs322785

Variant names:

• chr7-128115900-A-G
• rs322785

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 0.505 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
• Publications: 2 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 = 0.642 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

African (AFR) AF: 0.648 AC: 26892 AN: 41490

American (AMR) AF: 0.498 AC: 7624 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.498 AC: 1726 AN: 3466

East Asian (EAS) AF: 0.159 AC: 819 AN: 5166

South Asian (SAS) AF: 0.360 AC: 1739 AN: 4826

European-Finnish (FIN) AF: 0.408 AC: 4318 AN: 10586

Middle Eastern (MID) AF: 0.448 AC: 130 AN: 290

European-Non Finnish (NFE) AF: 0.471 AC: 32030 AN: 67952

Other (OTH) AF: 0.480 AC: 1011 AN: 2106

Alfa AF: 0.502 Hom.: 2548

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
PhyloP100		-0.58

Splicing

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

Other links and lift over

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