rs2997554

chr9-7448688-C-T

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

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

Gnomad4 AFR AF: 0.235

Gnomad4 AMR AF: 0.589

Gnomad4 ASJ AF: 0.529

Gnomad4 EAS AF: 0.514

Gnomad4 SAS AF: 0.573

Gnomad4 FIN AF: 0.546

Gnomad4 NFE AF: 0.572

Gnomad4 OTH AF: 0.471

Alfa AF: 0.452 Hom.: 2393

Bravo AF: 0.469

Asia WGS AF: 0.485 AC: 1687 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.40
Cadd	Benign	11
Dann	Benign	0.56

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2997554; hg19: chr9-7448688;