rs12195078

Variant names:

• chr6-89324073-C-T
• rs12195078

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 0.135 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
• Publications: 4 publications found

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.0632 AC: 2627 AN: 41552

American (AMR) AF: 0.173 AC: 2645 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.188 AC: 654 AN: 3470

East Asian (EAS) AF: 0.190 AC: 984 AN: 5180

South Asian (SAS) AF: 0.231 AC: 1111 AN: 4808

European-Finnish (FIN) AF: 0.142 AC: 1507 AN: 10584

Middle Eastern (MID) AF: 0.212 AC: 62 AN: 292

European-Non Finnish (NFE) AF: 0.153 AC: 10378 AN: 67988

Other (OTH) AF: 0.160 AC: 338 AN: 2108

Alfa AF: 0.150 Hom.: 1018

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
PhyloP100		-0.65

Splicing

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

Other links and lift over

dbSNP: rs12195078; hg19: chr6-90033792;