1-60349644-C-T

Position:

• chr1-60349644-C-T

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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

Gnomad4 AFR AF: 0.113

Gnomad4 AMR AF: 0.121

Gnomad4 ASJ AF: 0.132

Gnomad4 EAS AF: 0.375

Gnomad4 SAS AF: 0.146

Gnomad4 FIN AF: 0.0730

Gnomad4 NFE AF: 0.107

Gnomad4 OTH AF: 0.133

Alfa AF: 0.117 Hom.: 1457

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12137879; hg19: chr1-60815316;