chr12-60653100-T-C

Variant names:

• chr12-60653100-T-C
• rs1875726

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 0.287 in 152,048 control chromosomes in the GnomAD database, including 7,838 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 0.29 (7838 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.590
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.78).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.495 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: 0.287 AC: 43597 AN: 151930 Hom.: 7822 Cov.: 33

Gnomad AFR AF: 0.500

Gnomad AMI AF: 0.192

Gnomad AMR AF: 0.296

Gnomad ASJ AF: 0.147

Gnomad EAS AF: 0.381

Gnomad SAS AF: 0.236

Gnomad FIN AF: 0.200

Gnomad MID AF: 0.226

Gnomad NFE AF: 0.175

Gnomad OTH AF: 0.263

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

GnomAD4 genome AF: 0.287 AC: 43659 AN: 152048 Hom.: 7838 Cov.: 33 AF XY: 0.287 AC XY: 21361 AN XY: 74332

African (AFR) AF: 0.500 AC: 20731 AN: 41444

American (AMR) AF: 0.296 AC: 4531 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.147 AC: 510 AN: 3462

East Asian (EAS) AF: 0.381 AC: 1970 AN: 5170

South Asian (SAS) AF: 0.237 AC: 1140 AN: 4820

European-Finnish (FIN) AF: 0.200 AC: 2122 AN: 10590

Middle Eastern (MID) AF: 0.233 AC: 68 AN: 292

European-Non Finnish (NFE) AF: 0.175 AC: 11865 AN: 67964

Other (OTH) AF: 0.259 AC: 547 AN: 2112

Alfa AF: 0.235 Hom.: 692

Bravo AF: 0.307

Asia WGS AF: 0.324 AC: 1121 AN: 3452

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
CADD	Benign	6.6
DANN	Benign	0.81
PhyloP100		0.59

Splicing

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

Other links and lift over

dbSNP: rs1875726; hg19: chr12-61046881;