rs2006996

Positions:

• chr9-114830358-T-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.0765 in 152,264 control chromosomes in the GnomAD database, including 927 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 0.077 (927 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.399

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.308 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: 0.0764 AC: 11625 AN: 152146 Hom.: 925 Cov.: 32

Gnomad AFR AF: 0.0387

Gnomad AMI AF: 0.260

Gnomad AMR AF: 0.176

Gnomad ASJ AF: 0.0548

Gnomad EAS AF: 0.321

Gnomad SAS AF: 0.0919

Gnomad FIN AF: 0.144

Gnomad MID AF: 0.0348

Gnomad NFE AF: 0.0460

Gnomad OTH AF: 0.0631

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

GnomAD4 genome AF: 0.0765 AC: 11651 AN: 152264 Hom.: 927 Cov.: 32 AF XY: 0.0853 AC XY: 6350 AN XY: 74452

Gnomad4 AFR AF: 0.0388

Gnomad4 AMR AF: 0.176

Gnomad4 ASJ AF: 0.0548

Gnomad4 EAS AF: 0.321

Gnomad4 SAS AF: 0.0918

Gnomad4 FIN AF: 0.144

Gnomad4 NFE AF: 0.0460

Gnomad4 OTH AF: 0.0658

Alfa AF: 0.0593 Hom.: 1344

Bravo AF: 0.0810

Asia WGS AF: 0.176 AC: 612 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.40
DANN	Benign	0.53

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2006996; hg19: chr9-117592638;