rs4768491

Variant names:

• chr12-43234902-G-A
• rs4768491

Your query was ambiguous. Multiple possible variants found:

• chr12-43234902-G-A
• chr12-43234902-G-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 0.28 in 151,930 control chromosomes in the GnomAD database, including 6,233 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 0.28 (6233 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.434
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.41 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: 0.280 AC: 42448 AN: 151812 Hom.: 6225 Cov.: 31

Gnomad AFR AF: 0.368

Gnomad AMI AF: 0.188

Gnomad AMR AF: 0.232

Gnomad ASJ AF: 0.306

Gnomad EAS AF: 0.425

Gnomad SAS AF: 0.192

Gnomad FIN AF: 0.231

Gnomad MID AF: 0.313

Gnomad NFE AF: 0.239

Gnomad OTH AF: 0.283

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

GnomAD4 genome AF: 0.280 AC: 42481 AN: 151930 Hom.: 6233 Cov.: 31 AF XY: 0.278 AC XY: 20674 AN XY: 74288

African (AFR) AF: 0.368 AC: 15260 AN: 41436

American (AMR) AF: 0.231 AC: 3522 AN: 15254

Ashkenazi Jewish (ASJ) AF: 0.306 AC: 1058 AN: 3462

East Asian (EAS) AF: 0.425 AC: 2199 AN: 5176

South Asian (SAS) AF: 0.191 AC: 922 AN: 4824

European-Finnish (FIN) AF: 0.231 AC: 2445 AN: 10570

Middle Eastern (MID) AF: 0.320 AC: 94 AN: 294

European-Non Finnish (NFE) AF: 0.239 AC: 16207 AN: 67900

Other (OTH) AF: 0.287 AC: 603 AN: 2104

Alfa AF: 0.253 Hom.: 16109

Bravo AF: 0.282

Asia WGS AF: 0.337 AC: 1172 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	12
DANN	Benign	0.67
PhyloP100		-0.43

Splicing

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

Other links and lift over

dbSNP: rs4768491; hg19: chr12-43628705;