rs990708

Positions:

• chr9-31678814-C-T

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 0.241 in 151,662 control chromosomes in the GnomAD database, including 4,428 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 0.24 (4428 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.369

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.04).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.292 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: 0.241 AC: 36568 AN: 151544 Hom.: 4428 Cov.: 32

Gnomad AFR AF: 0.229

Gnomad AMI AF: 0.363

Gnomad AMR AF: 0.231

Gnomad ASJ AF: 0.215

Gnomad EAS AF: 0.242

Gnomad SAS AF: 0.303

Gnomad FIN AF: 0.249

Gnomad MID AF: 0.152

Gnomad NFE AF: 0.246

Gnomad OTH AF: 0.211

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

GnomAD4 genome AF: 0.241 AC: 36588 AN: 151662 Hom.: 4428 Cov.: 32 AF XY: 0.242 AC XY: 17897 AN XY: 74062

Gnomad4 AFR AF: 0.229

Gnomad4 AMR AF: 0.232

Gnomad4 ASJ AF: 0.215

Gnomad4 EAS AF: 0.242

Gnomad4 SAS AF: 0.304

Gnomad4 FIN AF: 0.249

Gnomad4 NFE AF: 0.246

Gnomad4 OTH AF: 0.209

Alfa AF: 0.243 Hom.: 2691

Bravo AF: 0.234

Asia WGS AF: 0.268 AC: 932 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.0
DANN	Benign	0.52

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs990708; hg19: chr9-31678812;