7-9283590-G-A

Variant names:

• chr7-9283590-G-A
• rs1919796

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 0.272 in 152,010 control chromosomes in the GnomAD database, including 7,842 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 0.27 (7842 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.330
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.51 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: 0.272 AC: 41312 AN: 151892 Hom.: 7823 Cov.: 33

Gnomad AFR AF: 0.516

Gnomad AMI AF: 0.0980

Gnomad AMR AF: 0.281

Gnomad ASJ AF: 0.132

Gnomad EAS AF: 0.468

Gnomad SAS AF: 0.156

Gnomad FIN AF: 0.183

Gnomad MID AF: 0.168

Gnomad NFE AF: 0.139

Gnomad OTH AF: 0.261

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

GnomAD4 genome AF: 0.272 AC: 41379 AN: 152010 Hom.: 7842 Cov.: 33 AF XY: 0.274 AC XY: 20370 AN XY: 74296

African (AFR) AF: 0.516 AC: 21386 AN: 41466

American (AMR) AF: 0.281 AC: 4289 AN: 15240

Ashkenazi Jewish (ASJ) AF: 0.132 AC: 459 AN: 3468

East Asian (EAS) AF: 0.467 AC: 2407 AN: 5150

South Asian (SAS) AF: 0.156 AC: 752 AN: 4816

European-Finnish (FIN) AF: 0.183 AC: 1941 AN: 10586

Middle Eastern (MID) AF: 0.177 AC: 52 AN: 294

European-Non Finnish (NFE) AF: 0.139 AC: 9447 AN: 67972

Other (OTH) AF: 0.264 AC: 557 AN: 2110

Alfa AF: 0.181 Hom.: 15131

Bravo AF: 0.294

Asia WGS AF: 0.333 AC: 1156 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.17
DANN	Benign	0.35
PhyloP100		-0.33

Splicing

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

Other links and lift over

dbSNP: rs1919796; hg19: chr7-9323220;