9-80504030-G-A

Variant names:

• chr9-80504030-G-A
• rs1972804

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The variant allele was found at a frequency of 0.325 in 151,892 control chromosomes in the GnomAD database, including 9,005 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 0.33 (9005 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.26
• Publications: 4 publications found

ACMG classification

Our verdict: Benign. The variant received -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.41).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.438 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.325 AC: 49399 AN: 151774 Hom.: 9003 Cov.: 32

Gnomad AFR AF: 0.186

Gnomad AMI AF: 0.555

Gnomad AMR AF: 0.447

Gnomad ASJ AF: 0.370

Gnomad EAS AF: 0.267

Gnomad SAS AF: 0.235

Gnomad FIN AF: 0.404

Gnomad MID AF: 0.364

Gnomad NFE AF: 0.376

Gnomad OTH AF: 0.348

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

GnomAD4 genome AF: 0.325 AC: 49420 AN: 151892 Hom.: 9005 Cov.: 32 AF XY: 0.327 AC XY: 24246 AN XY: 74236

African (AFR) AF: 0.186 AC: 7709 AN: 41452

American (AMR) AF: 0.447 AC: 6800 AN: 15224

Ashkenazi Jewish (ASJ) AF: 0.370 AC: 1282 AN: 3468

East Asian (EAS) AF: 0.267 AC: 1374 AN: 5150

South Asian (SAS) AF: 0.238 AC: 1147 AN: 4820

European-Finnish (FIN) AF: 0.404 AC: 4260 AN: 10538

Middle Eastern (MID) AF: 0.367 AC: 108 AN: 294

European-Non Finnish (NFE) AF: 0.376 AC: 25508 AN: 67928

Other (OTH) AF: 0.345 AC: 727 AN: 2108

Alfa AF: 0.369 Hom.: 14532

Bravo AF: 0.325

Asia WGS AF: 0.241 AC: 841 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.41
CADD	Benign	16
DANN	Benign	0.65
PhyloP100		2.3

Splicing

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

Other links and lift over

dbSNP: rs1972804; hg19: chr9-83118945;