rs9706509

Variant names:

• chr12-34657268-T-C
• rs9706509

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 6 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	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

African (AFR) AF: 0.0781 AC: 3228 AN: 41308

American (AMR) AF: 0.261 AC: 3904 AN: 14970

Ashkenazi Jewish (ASJ) AF: 0.300 AC: 1032 AN: 3440

East Asian (EAS) AF: 0.0150 AC: 77 AN: 5122

South Asian (SAS) AF: 0.256 AC: 1229 AN: 4796

European-Finnish (FIN) AF: 0.449 AC: 4737 AN: 10544

Middle Eastern (MID) AF: 0.381 AC: 112 AN: 294

European-Non Finnish (NFE) AF: 0.381 AC: 25477 AN: 66872

Other (OTH) AF: 0.265 AC: 551 AN: 2082

Alfa AF: 0.337 Hom.: 27947

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

Other links and lift over

dbSNP: rs9706509; hg19: chr12-34810203;