chr1-60370382-C-T

Variant names:

• chr1-60370382-C-T
• rs1414314

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 0.435 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
• Publications: 4 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

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

African (AFR) AF: 0.354 AC: 14656 AN: 41436

American (AMR) AF: 0.496 AC: 7577 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.411 AC: 1426 AN: 3472

East Asian (EAS) AF: 0.654 AC: 3373 AN: 5160

South Asian (SAS) AF: 0.603 AC: 2902 AN: 4816

European-Finnish (FIN) AF: 0.491 AC: 5180 AN: 10552

Middle Eastern (MID) AF: 0.476 AC: 140 AN: 294

European-Non Finnish (NFE) AF: 0.435 AC: 29548 AN: 67960

Other (OTH) AF: 0.445 AC: 940 AN: 2110

Alfa AF: 0.436 Hom.: 4661

Bravo AF: 0.429

Asia WGS AF: 0.603 AC: 2091 AN: 3468

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.25
DANN	Benign	0.79
PhyloP100		-1.4

Splicing

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

Other links and lift over

dbSNP: rs1414314; hg19: chr1-60836054;