rs1742500

Variant names:

• chr14-68863184-A-G
• rs1742500

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 0.639 in 152,016 control chromosomes in the GnomAD database, including 31,632 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 0.64 (31632 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.338

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.04).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.729 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: 0.639 AC: 97064 AN: 151898 Hom.: 31606 Cov.: 32

Gnomad AFR AF: 0.530

Gnomad AMI AF: 0.685

Gnomad AMR AF: 0.740

Gnomad ASJ AF: 0.642

Gnomad EAS AF: 0.525

Gnomad SAS AF: 0.692

Gnomad FIN AF: 0.654

Gnomad MID AF: 0.652

Gnomad NFE AF: 0.684

Gnomad OTH AF: 0.642

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

GnomAD4 genome AF: 0.639 AC: 97123 AN: 152016 Hom.: 31632 Cov.: 32 AF XY: 0.639 AC XY: 47488 AN XY: 74296

Gnomad4 AFR AF: 0.530

Gnomad4 AMR AF: 0.741

Gnomad4 ASJ AF: 0.642

Gnomad4 EAS AF: 0.524

Gnomad4 SAS AF: 0.692

Gnomad4 FIN AF: 0.654

Gnomad4 NFE AF: 0.684

Gnomad4 OTH AF: 0.646

Alfa AF: 0.672 Hom.: 54514

Bravo AF: 0.638

Asia WGS AF: 0.662 AC: 2300 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	4.3
DANN	Benign	0.70

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1742500; hg19: chr14-69329901;