rs9706509

Positions:

• chr12-34657268-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 0.27 in 150,336 control chromosomes in the GnomAD database, including 7,066 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 0.27 (7066 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: No conservation score assigned

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.377 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.271 AC: 40650 AN: 150218 Hom.: 7064 Cov.: 32

Gnomad AFR AF: 0.0784

Gnomad AMI AF: 0.328

Gnomad AMR AF: 0.261

Gnomad ASJ AF: 0.300

Gnomad EAS AF: 0.0150

Gnomad SAS AF: 0.255

Gnomad FIN AF: 0.449

Gnomad MID AF: 0.380

Gnomad NFE AF: 0.381

Gnomad OTH AF: 0.268

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

GnomAD4 genome AF: 0.270 AC: 40645 AN: 150336 Hom.: 7066 Cov.: 32 AF XY: 0.270 AC XY: 19866 AN XY: 73446

Gnomad4 AFR AF: 0.0781

Gnomad4 AMR AF: 0.261

Gnomad4 ASJ AF: 0.300

Gnomad4 EAS AF: 0.0150

Gnomad4 SAS AF: 0.256

Gnomad4 FIN AF: 0.449

Gnomad4 NFE AF: 0.381

Gnomad4 OTH AF: 0.265

Alfa AF: 0.354 Hom.: 12744

Bravo AF: 0.252

Asia WGS AF: 0.126 AC: 439 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	3.1
DANN	Benign	0.37

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9706509; hg19: chr12-34810203;