9-27583470-G-C

Variant names:

• chr9-27583470-G-C
• rs7864840

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 0.0594 in 152,146 control chromosomes in the GnomAD database, including 512 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 0.059 (512 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.767
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.147 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: 0.0593 AC: 9015 AN: 152034 Hom.: 511 Cov.: 32

Gnomad AFR AF: 0.150

Gnomad AMI AF: 0.0296

Gnomad AMR AF: 0.0259

Gnomad ASJ AF: 0.0257

Gnomad EAS AF: 0.000770

Gnomad SAS AF: 0.0369

Gnomad FIN AF: 0.00954

Gnomad MID AF: 0.0573

Gnomad NFE AF: 0.0278

Gnomad OTH AF: 0.0474

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

GnomAD4 genome AF: 0.0594 AC: 9039 AN: 152146 Hom.: 512 Cov.: 32 AF XY: 0.0550 AC XY: 4090 AN XY: 74392

African (AFR) AF: 0.150 AC: 6239 AN: 41504

American (AMR) AF: 0.0258 AC: 395 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.0257 AC: 89 AN: 3468

East Asian (EAS) AF: 0.000772 AC: 4 AN: 5182

South Asian (SAS) AF: 0.0374 AC: 180 AN: 4816

European-Finnish (FIN) AF: 0.00954 AC: 101 AN: 10582

Middle Eastern (MID) AF: 0.0548 AC: 16 AN: 292

European-Non Finnish (NFE) AF: 0.0278 AC: 1888 AN: 67990

Other (OTH) AF: 0.0474 AC: 100 AN: 2108

Alfa AF: 0.0470 Hom.: 50

Bravo AF: 0.0643

Asia WGS AF: 0.0340 AC: 118 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	5.0
DANN	Benign	0.66
PhyloP100		0.77

Splicing

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

Other links and lift over

dbSNP: rs7864840; hg19: chr9-27583468;