rs3176806

Variant names:

• chr12-9751478-C-A
• rs3176806

Your query was ambiguous. Multiple possible variants found:

• chr12-9751478-C-A
• chr12-9751478-C-G
• chr12-9751478-C-T

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 0.252 in 151,876 control chromosomes in the GnomAD database, including 5,003 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 0.25 (5003 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.104
• Publications: 5 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.264 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: 0.252 AC: 38213 AN: 151756 Hom.: 5002 Cov.: 31

Gnomad AFR AF: 0.264

Gnomad AMI AF: 0.457

Gnomad AMR AF: 0.249

Gnomad ASJ AF: 0.212

Gnomad EAS AF: 0.0477

Gnomad SAS AF: 0.171

Gnomad FIN AF: 0.241

Gnomad MID AF: 0.199

Gnomad NFE AF: 0.268

Gnomad OTH AF: 0.241

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

GnomAD4 genome AF: 0.252 AC: 38253 AN: 151876 Hom.: 5003 Cov.: 31 AF XY: 0.249 AC XY: 18497 AN XY: 74232

African (AFR) AF: 0.265 AC: 10953 AN: 41408

American (AMR) AF: 0.250 AC: 3803 AN: 15236

Ashkenazi Jewish (ASJ) AF: 0.212 AC: 734 AN: 3468

East Asian (EAS) AF: 0.0480 AC: 248 AN: 5168

South Asian (SAS) AF: 0.171 AC: 825 AN: 4826

European-Finnish (FIN) AF: 0.241 AC: 2533 AN: 10528

Middle Eastern (MID) AF: 0.195 AC: 57 AN: 292

European-Non Finnish (NFE) AF: 0.268 AC: 18181 AN: 67936

Other (OTH) AF: 0.239 AC: 504 AN: 2106

Alfa AF: 0.159 Hom.: 332

Bravo AF: 0.252

Asia WGS AF: 0.125 AC: 436 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	5.1
DANN	Benign	0.58
PhyloP100		0.10

Splicing

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

Other links and lift over

dbSNP: rs3176806; hg19: chr12-9904074;