rs2006996

Variant names:

• chr9-114830358-T-C
• rs2006996

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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;