rs3742555

chr14-53918751-A-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 0.107 in 152,026 control chromosomes in the GnomAD database, including 998 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 0.11 (998 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0770

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 (SAS) allele frequency at 95% confidence interval = 0.18 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.107 AC: 16285 AN: 151910 Hom.: 991 Cov.: 32

Gnomad AFR AF: 0.156

Gnomad AMI AF: 0.0329

Gnomad AMR AF: 0.110

Gnomad ASJ AF: 0.0905

Gnomad EAS AF: 0.103

Gnomad SAS AF: 0.191

Gnomad FIN AF: 0.113

Gnomad MID AF: 0.0854

Gnomad NFE AF: 0.0728

Gnomad OTH AF: 0.0872

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

GnomAD4 genome AF: 0.107 AC: 16326 AN: 152026 Hom.: 998 Cov.: 32 AF XY: 0.111 AC XY: 8250 AN XY: 74308

Gnomad4 AFR AF: 0.157

Gnomad4 AMR AF: 0.110

Gnomad4 ASJ AF: 0.0905

Gnomad4 EAS AF: 0.103

Gnomad4 SAS AF: 0.191

Gnomad4 FIN AF: 0.113

Gnomad4 NFE AF: 0.0728

Gnomad4 OTH AF: 0.0919

Alfa AF: 0.105 Hom.: 123

Bravo AF: 0.104

Asia WGS AF: 0.171 AC: 594 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	0.49
Dann	Benign	0.66

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3742555; hg19: chr14-54385469;