rs12175268

Variant names:

• chr6-13560413-C-G
• rs12175268

Your query was ambiguous. Multiple possible variants found:

• chr6-13560413-C-G
• chr6-13560413-C-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 0.13 in 152,160 control chromosomes in the GnomAD database, including 1,595 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 (1595 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.893
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.248 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: 0.130 AC: 19733 AN: 152040 Hom.: 1595 Cov.: 32

Gnomad AFR AF: 0.0488

Gnomad AMI AF: 0.179

Gnomad AMR AF: 0.104

Gnomad ASJ AF: 0.196

Gnomad EAS AF: 0.259

Gnomad SAS AF: 0.210

Gnomad FIN AF: 0.198

Gnomad MID AF: 0.146

Gnomad NFE AF: 0.155

Gnomad OTH AF: 0.124

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

GnomAD4 genome AF: 0.130 AC: 19720 AN: 152160 Hom.: 1595 Cov.: 32 AF XY: 0.134 AC XY: 9951 AN XY: 74380

African (AFR) AF: 0.0486 AC: 2019 AN: 41516

American (AMR) AF: 0.104 AC: 1594 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.196 AC: 681 AN: 3468

East Asian (EAS) AF: 0.259 AC: 1343 AN: 5182

South Asian (SAS) AF: 0.210 AC: 1009 AN: 4814

European-Finnish (FIN) AF: 0.198 AC: 2092 AN: 10570

Middle Eastern (MID) AF: 0.150 AC: 44 AN: 294

European-Non Finnish (NFE) AF: 0.155 AC: 10517 AN: 68000

Other (OTH) AF: 0.122 AC: 258 AN: 2116

Alfa AF: 0.0849 Hom.: 125

Bravo AF: 0.120

Asia WGS AF: 0.198 AC: 685 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.31
DANN	Benign	0.53
PhyloP100		-0.89

Splicing

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

Other links and lift over

dbSNP: rs12175268; hg19: chr6-13560645;