1-60370382-C-T

Variant names:

• chr1-60370382-C-T
• rs1414314

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 0.435 in 151,974 control chromosomes in the GnomAD database, including 14,817 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 0.44 (14817 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.44

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.635 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: 0.435 AC: 66082 AN: 151856 Hom.: 14800 Cov.: 33

Gnomad AFR AF: 0.354

Gnomad AMI AF: 0.418

Gnomad AMR AF: 0.496

Gnomad ASJ AF: 0.411

Gnomad EAS AF: 0.654

Gnomad SAS AF: 0.601

Gnomad FIN AF: 0.491

Gnomad MID AF: 0.472

Gnomad NFE AF: 0.435

Gnomad OTH AF: 0.439

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

GnomAD4 genome AF: 0.435 AC: 66122 AN: 151974 Hom.: 14817 Cov.: 33 AF XY: 0.443 AC XY: 32880 AN XY: 74270

Gnomad4 AFR AF: 0.354

Gnomad4 AMR AF: 0.496

Gnomad4 ASJ AF: 0.411

Gnomad4 EAS AF: 0.654

Gnomad4 SAS AF: 0.603

Gnomad4 FIN AF: 0.491

Gnomad4 NFE AF: 0.435

Gnomad4 OTH AF: 0.445

Alfa AF: 0.418 Hom.: 2049

Bravo AF: 0.429

Asia WGS AF: 0.603 AC: 2091 AN: 3468

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.25
DANN	Benign	0.79

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1414314; hg19: chr1-60836054;