rs7139228

Positions:

• chr12-91119534-G-A
• chr12-91119534-G-T

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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

Gnomad4 AFR AF: 0.203

Gnomad4 AMR AF: 0.0767

Gnomad4 ASJ AF: 0.146

Gnomad4 EAS AF: 0.0606

Gnomad4 SAS AF: 0.0415

Gnomad4 FIN AF: 0.0440

Gnomad4 NFE AF: 0.0684

Gnomad4 OTH AF: 0.105

Alfa AF: 0.0577 Hom.: 96

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7139228; hg19: chr12-91513311;