chr14-60355944-C-T

Variant names:

• chr14-60355944-C-T
• rs1266416

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 0.355 in 151,916 control chromosomes in the GnomAD database, including 10,621 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 0.36 (10621 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.803
• Publications: 5 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 = 0.685 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: 0.355 AC: 53926 AN: 151798 Hom.: 10605 Cov.: 31

Gnomad AFR AF: 0.477

Gnomad AMI AF: 0.254

Gnomad AMR AF: 0.283

Gnomad ASJ AF: 0.326

Gnomad EAS AF: 0.706

Gnomad SAS AF: 0.449

Gnomad FIN AF: 0.186

Gnomad MID AF: 0.443

Gnomad NFE AF: 0.293

Gnomad OTH AF: 0.367

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

GnomAD4 genome AF: 0.355 AC: 53977 AN: 151916 Hom.: 10621 Cov.: 31 AF XY: 0.354 AC XY: 26245 AN XY: 74224

African (AFR) AF: 0.477 AC: 19753 AN: 41406

American (AMR) AF: 0.283 AC: 4315 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.326 AC: 1131 AN: 3466

East Asian (EAS) AF: 0.705 AC: 3633 AN: 5156

South Asian (SAS) AF: 0.447 AC: 2156 AN: 4824

European-Finnish (FIN) AF: 0.186 AC: 1964 AN: 10548

Middle Eastern (MID) AF: 0.438 AC: 128 AN: 292

European-Non Finnish (NFE) AF: 0.293 AC: 19882 AN: 67948

Other (OTH) AF: 0.373 AC: 784 AN: 2104

Alfa AF: 0.293 Hom.: 3515

Bravo AF: 0.367

Asia WGS AF: 0.568 AC: 1973 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.33
DANN	Benign	0.18
PhyloP100		-0.80

Splicing

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

Other links and lift over

dbSNP: rs1266416; hg19: chr14-60822662;