1-60406619-C-T

Position:

• chr1-60406619-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 0.0854 in 152,096 control chromosomes in the GnomAD database, including 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 0.085 (595 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.650

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.115 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: 0.0854 AC: 12982 AN: 151980 Hom.: 596 Cov.: 32

Gnomad AFR AF: 0.0726

Gnomad AMI AF: 0.0965

Gnomad AMR AF: 0.0656

Gnomad ASJ AF: 0.154

Gnomad EAS AF: 0.00193

Gnomad SAS AF: 0.123

Gnomad FIN AF: 0.0880

Gnomad MID AF: 0.114

Gnomad NFE AF: 0.0971

Gnomad OTH AF: 0.0851

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

GnomAD4 genome AF: 0.0854 AC: 12986 AN: 152096 Hom.: 595 Cov.: 32 AF XY: 0.0860 AC XY: 6396 AN XY: 74366

Gnomad4 AFR AF: 0.0726

Gnomad4 AMR AF: 0.0655

Gnomad4 ASJ AF: 0.154

Gnomad4 EAS AF: 0.00193

Gnomad4 SAS AF: 0.123

Gnomad4 FIN AF: 0.0880

Gnomad4 NFE AF: 0.0972

Gnomad4 OTH AF: 0.0837

Alfa AF: 0.102 Hom.: 348

Bravo AF: 0.0819

Asia WGS AF: 0.0580 AC: 202 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.77
DANN	Benign	0.21

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs298157; hg19: chr1-60872291;