14-60606157-T-C

Variant names:

• chr14-60606157-T-C
• rs10483727

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 0.456 in 152,230 control chromosomes in the GnomAD database, including 19,819 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 0.46 (19819 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.639

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.6 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: 0.456 AC: 69357 AN: 152112 Hom.: 19813 Cov.: 32

Gnomad AFR AF: 0.118

Gnomad AMI AF: 0.560

Gnomad AMR AF: 0.592

Gnomad ASJ AF: 0.508

Gnomad EAS AF: 0.231

Gnomad SAS AF: 0.431

Gnomad FIN AF: 0.728

Gnomad MID AF: 0.367

Gnomad NFE AF: 0.605

Gnomad OTH AF: 0.435

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

GnomAD4 genome AF: 0.456 AC: 69380 AN: 152230 Hom.: 19819 Cov.: 32 AF XY: 0.462 AC XY: 34381 AN XY: 74428

Gnomad4 AFR AF: 0.118

Gnomad4 AMR AF: 0.593

Gnomad4 ASJ AF: 0.508

Gnomad4 EAS AF: 0.232

Gnomad4 SAS AF: 0.433

Gnomad4 FIN AF: 0.728

Gnomad4 NFE AF: 0.605

Gnomad4 OTH AF: 0.433

Alfa AF: 0.558 Hom.: 53135

Bravo AF: 0.432

Asia WGS AF: 0.333 AC: 1159 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	5.4
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: rs10483727; hg19: chr14-61072875;