1-60349644-C-T

Variant names:

• chr1-60349644-C-T
• rs12137879

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 0.119 in 152,134 control chromosomes in the GnomAD database, including 1,323 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 0.12 (1323 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.217
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.361 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: 0.119 AC: 18047 AN: 152014 Hom.: 1319 Cov.: 32

Gnomad AFR AF: 0.113

Gnomad AMI AF: 0.0680

Gnomad AMR AF: 0.121

Gnomad ASJ AF: 0.132

Gnomad EAS AF: 0.375

Gnomad SAS AF: 0.147

Gnomad FIN AF: 0.0730

Gnomad MID AF: 0.174

Gnomad NFE AF: 0.107

Gnomad OTH AF: 0.133

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

GnomAD4 genome AF: 0.119 AC: 18061 AN: 152134 Hom.: 1323 Cov.: 32 AF XY: 0.119 AC XY: 8815 AN XY: 74354

African (AFR) AF: 0.113 AC: 4681 AN: 41510

American (AMR) AF: 0.121 AC: 1852 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.132 AC: 457 AN: 3468

East Asian (EAS) AF: 0.375 AC: 1938 AN: 5166

South Asian (SAS) AF: 0.146 AC: 706 AN: 4824

European-Finnish (FIN) AF: 0.0730 AC: 774 AN: 10596

Middle Eastern (MID) AF: 0.184 AC: 54 AN: 294

European-Non Finnish (NFE) AF: 0.107 AC: 7256 AN: 67990

Other (OTH) AF: 0.133 AC: 281 AN: 2112

Alfa AF: 0.117 Hom.: 1804

Bravo AF: 0.125

Asia WGS AF: 0.214 AC: 744 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	5.6
DANN	Benign	0.65
PhyloP100		0.22

Splicing

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

Other links and lift over

dbSNP: rs12137879; hg19: chr1-60815316;