rs76270203

Variant names:

• chr12-113499191-A-C
• rs76270203

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 0.0264 in 152,246 control chromosomes in the GnomAD database, including 87 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 0.026 (87 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.92
• Publications: 2 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 (SAS) allele frequency at 95% confidence interval = 0.0622 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: 0.0263 AC: 4002 AN: 152128 Hom.: 85 Cov.: 32

Gnomad AFR AF: 0.00770

Gnomad AMI AF: 0.00110

Gnomad AMR AF: 0.0376

Gnomad ASJ AF: 0.0458

Gnomad EAS AF: 0.0396

Gnomad SAS AF: 0.0668

Gnomad FIN AF: 0.0391

Gnomad MID AF: 0.0411

Gnomad NFE AF: 0.0286

Gnomad OTH AF: 0.0234

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

GnomAD4 genome AF: 0.0264 AC: 4017 AN: 152246 Hom.: 87 Cov.: 32 AF XY: 0.0277 AC XY: 2061 AN XY: 74446

African (AFR) AF: 0.00770 AC: 320 AN: 41546

American (AMR) AF: 0.0376 AC: 575 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.0458 AC: 159 AN: 3470

East Asian (EAS) AF: 0.0399 AC: 207 AN: 5184

South Asian (SAS) AF: 0.0683 AC: 329 AN: 4818

European-Finnish (FIN) AF: 0.0391 AC: 415 AN: 10614

Middle Eastern (MID) AF: 0.0408 AC: 12 AN: 294

European-Non Finnish (NFE) AF: 0.0286 AC: 1944 AN: 67996

Other (OTH) AF: 0.0260 AC: 55 AN: 2112

Alfa AF: 0.0285 Hom.: 19

Bravo AF: 0.0250

Asia WGS AF: 0.0680 AC: 235 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.16
DANN	Benign	0.66
PhyloP100		-2.9

Splicing

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

Other links and lift over

dbSNP: rs76270203; hg19: chr12-113936996;