9-7445627-C-G

Variant names:

• chr9-7445627-C-G
• rs2997549

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 0.583 in 147,282 control chromosomes in the GnomAD database, including 25,661 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 0.58 (25661 hom., cov: 25)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0510
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.699 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.583 AC: 85783 AN: 147194 Hom.: 25645 Cov.: 25

Gnomad AFR AF: 0.413

Gnomad AMI AF: 0.847

Gnomad AMR AF: 0.679

Gnomad ASJ AF: 0.633

Gnomad EAS AF: 0.629

Gnomad SAS AF: 0.718

Gnomad FIN AF: 0.652

Gnomad MID AF: 0.690

Gnomad NFE AF: 0.630

Gnomad OTH AF: 0.585

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

GnomAD4 genome AF: 0.583 AC: 85822 AN: 147282 Hom.: 25661 Cov.: 25 AF XY: 0.587 AC XY: 42013 AN XY: 71626

African (AFR) AF: 0.412 AC: 16092 AN: 39018

American (AMR) AF: 0.679 AC: 10061 AN: 14808

Ashkenazi Jewish (ASJ) AF: 0.633 AC: 2185 AN: 3450

East Asian (EAS) AF: 0.630 AC: 3141 AN: 4988

South Asian (SAS) AF: 0.719 AC: 3379 AN: 4700

European-Finnish (FIN) AF: 0.652 AC: 6249 AN: 9586

Middle Eastern (MID) AF: 0.694 AC: 197 AN: 284

European-Non Finnish (NFE) AF: 0.630 AC: 42543 AN: 67496

Other (OTH) AF: 0.590 AC: 1204 AN: 2042

Alfa AF: 0.593 Hom.: 3276

Bravo AF: 0.565

Asia WGS AF: 0.650 AC: 2259 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	1.4
DANN	Benign	0.28
PhyloP100		0.051

Splicing

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

Other links and lift over

dbSNP: rs2997549; hg19: chr9-7445627; COSMIC: COSV60325833;