rs12660547

Variant names:

• chr6-138126925-T-C
• rs12660547

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 0.248 in 152,124 control chromosomes in the GnomAD database, including 4,935 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 0.25 (4935 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.308
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.4 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: 0.248 AC: 37665 AN: 152004 Hom.: 4918 Cov.: 33

Gnomad AFR AF: 0.234

Gnomad AMI AF: 0.236

Gnomad AMR AF: 0.217

Gnomad ASJ AF: 0.282

Gnomad EAS AF: 0.185

Gnomad SAS AF: 0.415

Gnomad FIN AF: 0.143

Gnomad MID AF: 0.335

Gnomad NFE AF: 0.270

Gnomad OTH AF: 0.263

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

GnomAD4 genome AF: 0.248 AC: 37716 AN: 152124 Hom.: 4935 Cov.: 33 AF XY: 0.244 AC XY: 18145 AN XY: 74358

African (AFR) AF: 0.234 AC: 9716 AN: 41478

American (AMR) AF: 0.216 AC: 3306 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.282 AC: 978 AN: 3472

East Asian (EAS) AF: 0.185 AC: 960 AN: 5184

South Asian (SAS) AF: 0.415 AC: 2000 AN: 4818

European-Finnish (FIN) AF: 0.143 AC: 1514 AN: 10588

Middle Eastern (MID) AF: 0.316 AC: 93 AN: 294

European-Non Finnish (NFE) AF: 0.270 AC: 18363 AN: 67990

Other (OTH) AF: 0.271 AC: 571 AN: 2110

Alfa AF: 0.272 Hom.: 7901

Bravo AF: 0.247

Asia WGS AF: 0.328 AC: 1140 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.41
DANN	Benign	0.56
PhyloP100		-0.31

Splicing

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

Other links and lift over

dbSNP: rs12660547; hg19: chr6-138448062;