rs1742500

Variant names:

• chr14-68863184-A-G
• rs1742500

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 0.639 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
• Publications: 5 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

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

African (AFR) AF: 0.530 AC: 21972 AN: 41446

American (AMR) AF: 0.741 AC: 11316 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.642 AC: 2225 AN: 3468

East Asian (EAS) AF: 0.524 AC: 2710 AN: 5168

South Asian (SAS) AF: 0.692 AC: 3335 AN: 4822

European-Finnish (FIN) AF: 0.654 AC: 6896 AN: 10540

Middle Eastern (MID) AF: 0.636 AC: 187 AN: 294

European-Non Finnish (NFE) AF: 0.684 AC: 46499 AN: 67988

Other (OTH) AF: 0.646 AC: 1358 AN: 2102

Alfa AF: 0.667 Hom.: 126889

Bravo AF: 0.638

Asia WGS AF: 0.662 AC: 2300 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	4.3
DANN	Benign	0.70
PhyloP100		0.34

Splicing

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

Other links and lift over

dbSNP: rs1742500; hg19: chr14-69329901;