rs7139228

Variant names:

• chr12-91119534-G-A
• rs7139228

Your query was ambiguous. Multiple possible variants found:

• chr12-91119534-G-A
• chr12-91119534-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 0.105 in 152,114 control chromosomes in the GnomAD database, including 1,159 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 0.11 (1159 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.208
• Publications: 7 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.199 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: 0.105 AC: 15993 AN: 151996 Hom.: 1150 Cov.: 32

Gnomad AFR AF: 0.203

Gnomad AMI AF: 0.0549

Gnomad AMR AF: 0.0768

Gnomad ASJ AF: 0.146

Gnomad EAS AF: 0.0607

Gnomad SAS AF: 0.0417

Gnomad FIN AF: 0.0440

Gnomad MID AF: 0.111

Gnomad NFE AF: 0.0685

Gnomad OTH AF: 0.101

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

GnomAD4 genome AF: 0.105 AC: 16038 AN: 152114 Hom.: 1159 Cov.: 32 AF XY: 0.102 AC XY: 7599 AN XY: 74372

African (AFR) AF: 0.203 AC: 8421 AN: 41478

American (AMR) AF: 0.0767 AC: 1172 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.146 AC: 507 AN: 3468

East Asian (EAS) AF: 0.0606 AC: 314 AN: 5178

South Asian (SAS) AF: 0.0415 AC: 200 AN: 4814

European-Finnish (FIN) AF: 0.0440 AC: 467 AN: 10610

Middle Eastern (MID) AF: 0.116 AC: 34 AN: 294

European-Non Finnish (NFE) AF: 0.0684 AC: 4652 AN: 67968

Other (OTH) AF: 0.105 AC: 221 AN: 2114

Alfa AF: 0.0618 Hom.: 105

Bravo AF: 0.113

Asia WGS AF: 0.0600 AC: 209 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.032
DANN	Benign	0.62
PhyloP100		-0.21

Splicing

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

Other links and lift over

dbSNP: rs7139228; hg19: chr12-91513311;