rs12195078

Variant names:

• chr6-89324073-C-T
• rs12195078

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 0.135 in 152,186 control chromosomes in the GnomAD database, including 1,560 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 0.13 (1560 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.653

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.79).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.22 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: 0.135 AC: 20501 AN: 152068 Hom.: 1561 Cov.: 32

Gnomad AFR AF: 0.0633

Gnomad AMI AF: 0.226

Gnomad AMR AF: 0.173

Gnomad ASJ AF: 0.188

Gnomad EAS AF: 0.190

Gnomad SAS AF: 0.232

Gnomad FIN AF: 0.142

Gnomad MID AF: 0.210

Gnomad NFE AF: 0.153

Gnomad OTH AF: 0.154

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

GnomAD4 genome AF: 0.135 AC: 20512 AN: 152186 Hom.: 1560 Cov.: 32 AF XY: 0.138 AC XY: 10284 AN XY: 74406

Gnomad4 AFR AF: 0.0632

Gnomad4 AMR AF: 0.173

Gnomad4 ASJ AF: 0.188

Gnomad4 EAS AF: 0.190

Gnomad4 SAS AF: 0.231

Gnomad4 FIN AF: 0.142

Gnomad4 NFE AF: 0.153

Gnomad4 OTH AF: 0.160

Alfa AF: 0.151 Hom.: 946

Bravo AF: 0.132

Asia WGS AF: 0.219 AC: 761 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	8.4
DANN	Benign	0.85

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12195078; hg19: chr6-90033792;