rs4902661

Positions:

• chr14-68870464-C-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 0.688 in 145,818 control chromosomes in the GnomAD database, including 34,782 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 0.69 (34782 hom., cov: 25)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.270

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.72).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.756 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.68870464C>T		intergenic_region

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.688 AC: 100277 AN: 145770 Hom.: 34769 Cov.: 25

Gnomad AFR AF: 0.673

Gnomad AMI AF: 0.711

Gnomad AMR AF: 0.768

Gnomad ASJ AF: 0.724

Gnomad EAS AF: 0.498

Gnomad SAS AF: 0.749

Gnomad FIN AF: 0.644

Gnomad MID AF: 0.686

Gnomad NFE AF: 0.692

Gnomad OTH AF: 0.688

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

GnomAD4 genome AF: 0.688 AC: 100304 AN: 145818 Hom.: 34782 Cov.: 25 AF XY: 0.688 AC XY: 48519 AN XY: 70528

Gnomad4 AFR AF: 0.673

Gnomad4 AMR AF: 0.768

Gnomad4 ASJ AF: 0.724

Gnomad4 EAS AF: 0.498

Gnomad4 SAS AF: 0.749

Gnomad4 FIN AF: 0.644

Gnomad4 NFE AF: 0.692

Gnomad4 OTH AF: 0.691

Alfa AF: 0.692 Hom.: 7376

Bravo AF: 0.695

Asia WGS AF: 0.696 AC: 2407 AN: 3460

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.72
CADD	Benign	6.0
DANN	Benign	0.74

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4902661; hg19: chr14-69337181;