rs7296288

Variant names:

• chr12-49086185-A-C
• rs7296288

Your query was ambiguous. Multiple possible variants found:

• chr12-49086185-A-C
• chr12-49086185-A-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 0.501 in 152,080 control chromosomes in the GnomAD database, including 19,420 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 0.50 (19420 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.94
• Publications: 26 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 (AFR) allele frequency at 95% confidence interval = 0.571 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.501 AC: 76060 AN: 151960 Hom.: 19380 Cov.: 32

Gnomad AFR AF: 0.576

Gnomad AMI AF: 0.506

Gnomad AMR AF: 0.408

Gnomad ASJ AF: 0.364

Gnomad EAS AF: 0.424

Gnomad SAS AF: 0.545

Gnomad FIN AF: 0.543

Gnomad MID AF: 0.364

Gnomad NFE AF: 0.480

Gnomad OTH AF: 0.450

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

GnomAD4 genome AF: 0.501 AC: 76162 AN: 152080 Hom.: 19420 Cov.: 32 AF XY: 0.502 AC XY: 37287 AN XY: 74334

African (AFR) AF: 0.577 AC: 23947 AN: 41488

American (AMR) AF: 0.408 AC: 6239 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.364 AC: 1264 AN: 3468

East Asian (EAS) AF: 0.424 AC: 2194 AN: 5174

South Asian (SAS) AF: 0.546 AC: 2634 AN: 4824

European-Finnish (FIN) AF: 0.543 AC: 5735 AN: 10564

Middle Eastern (MID) AF: 0.364 AC: 107 AN: 294

European-Non Finnish (NFE) AF: 0.480 AC: 32636 AN: 67964

Other (OTH) AF: 0.448 AC: 947 AN: 2112

Alfa AF: 0.475 Hom.: 71225

Bravo AF: 0.484

Asia WGS AF: 0.481 AC: 1671 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.046
DANN	Benign	0.71
PhyloP100		-3.9

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs7296288;

hg19: chr12-49479968;