rs1959290

Positions:

• chr14-86672385-T-C

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 0.177 in 152,066 control chromosomes in the GnomAD database, including 2,629 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 0.18 (2629 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.768

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.216 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: 0.177 AC: 26888 AN: 151948 Hom.: 2630 Cov.: 32

Gnomad AFR AF: 0.121

Gnomad AMI AF: 0.206

Gnomad AMR AF: 0.131

Gnomad ASJ AF: 0.230

Gnomad EAS AF: 0.0133

Gnomad SAS AF: 0.127

Gnomad FIN AF: 0.275

Gnomad MID AF: 0.155

Gnomad NFE AF: 0.219

Gnomad OTH AF: 0.170

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

GnomAD4 genome AF: 0.177 AC: 26893 AN: 152066 Hom.: 2629 Cov.: 32 AF XY: 0.175 AC XY: 13022 AN XY: 74304

Gnomad4 AFR AF: 0.121

Gnomad4 AMR AF: 0.130

Gnomad4 ASJ AF: 0.230

Gnomad4 EAS AF: 0.0134

Gnomad4 SAS AF: 0.128

Gnomad4 FIN AF: 0.275

Gnomad4 NFE AF: 0.219

Gnomad4 OTH AF: 0.168

Alfa AF: 0.213 Hom.: 449

Bravo AF: 0.162

Asia WGS AF: 0.0800 AC: 279 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	2.5
DANN	Benign	0.78

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1959290; hg19: chr14-87138729;