rs1958781

Positions:

• chr14-49366783-C-A

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 0.448 in 151,964 control chromosomes in the GnomAD database, including 15,843 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 0.45 (15843 hom., cov: 31)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.605

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.477 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.49366783C>A		intergenic_region

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.448 AC: 67955 AN: 151850 Hom.: 15826 Cov.: 31

Gnomad AFR AF: 0.482

Gnomad AMI AF: 0.576

Gnomad AMR AF: 0.449

Gnomad ASJ AF: 0.448

Gnomad EAS AF: 0.00693

Gnomad SAS AF: 0.226

Gnomad FIN AF: 0.464

Gnomad MID AF: 0.402

Gnomad NFE AF: 0.471

Gnomad OTH AF: 0.443

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

GnomAD4 genome AF: 0.448 AC: 68012 AN: 151964 Hom.: 15843 Cov.: 31 AF XY: 0.440 AC XY: 32679 AN XY: 74282

Gnomad4 AFR AF: 0.482

Gnomad4 AMR AF: 0.449

Gnomad4 ASJ AF: 0.448

Gnomad4 EAS AF: 0.00694

Gnomad4 SAS AF: 0.227

Gnomad4 FIN AF: 0.464

Gnomad4 NFE AF: 0.471

Gnomad4 OTH AF: 0.439

Alfa AF: 0.462 Hom.: 3959

Bravo AF: 0.449

Asia WGS AF: 0.158 AC: 551 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.33
DANN	Benign	0.31

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1958781; hg19: chr14-49833501;