rs2997554

Variant names:

• chr9-7448688-C-T
• rs2997554

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 0.477 in 152,000 control chromosomes in the GnomAD database, including 19,061 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 0.48 (19061 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.610
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.4).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.579 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.478 AC: 72527 AN: 151880 Hom.: 19056 Cov.: 32

Gnomad AFR AF: 0.235

Gnomad AMI AF: 0.832

Gnomad AMR AF: 0.589

Gnomad ASJ AF: 0.529

Gnomad EAS AF: 0.514

Gnomad SAS AF: 0.573

Gnomad FIN AF: 0.546

Gnomad MID AF: 0.563

Gnomad NFE AF: 0.572

Gnomad OTH AF: 0.472

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

GnomAD4 genome AF: 0.477 AC: 72542 AN: 152000 Hom.: 19061 Cov.: 32 AF XY: 0.479 AC XY: 35584 AN XY: 74296

African (AFR) AF: 0.235 AC: 9742 AN: 41440

American (AMR) AF: 0.589 AC: 9005 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.529 AC: 1834 AN: 3470

East Asian (EAS) AF: 0.514 AC: 2646 AN: 5152

South Asian (SAS) AF: 0.573 AC: 2766 AN: 4826

European-Finnish (FIN) AF: 0.546 AC: 5755 AN: 10544

Middle Eastern (MID) AF: 0.575 AC: 169 AN: 294

European-Non Finnish (NFE) AF: 0.572 AC: 38873 AN: 67964

Other (OTH) AF: 0.471 AC: 995 AN: 2112

Alfa AF: 0.475 Hom.: 3622

Bravo AF: 0.469

Asia WGS AF: 0.485 AC: 1687 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.40
CADD	Benign	11
DANN	Benign	0.56
PhyloP100		0.61

Splicing

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

Other links and lift over

dbSNP: rs2997554; hg19: chr9-7448688;