rs1459148

Positions:

• chr14-98374106-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The variant allele was found at a frequency of 0.016 in 152,268 control chromosomes in the GnomAD database, including 38 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 0.016 (38 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.200

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BS1: Variant frequency is greater than expected in population nfe. gnomad4 allele frequency = 0.016 (2431/152268) while in subpopulation NFE AF= 0.0233 (1588/68022). AF 95% confidence interval is 0.0224. There are 38 homozygotes in gnomad4. There are 1133 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
• BS2: High Homozygotes in GnomAd4 at 38 gene

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: 0.0160 AC: 2429 AN: 152150 Hom.: 38 Cov.: 32

Gnomad AFR AF: 0.00405

Gnomad AMI AF: 0.0340

Gnomad AMR AF: 0.0208

Gnomad ASJ AF: 0.0182

Gnomad EAS AF: 0.000578

Gnomad SAS AF: 0.0162

Gnomad FIN AF: 0.0147

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.0233

Gnomad OTH AF: 0.0120

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

GnomAD4 genome AF: 0.0160 AC: 2431 AN: 152268 Hom.: 38 Cov.: 32 AF XY: 0.0152 AC XY: 1133 AN XY: 74442

Gnomad4 AFR AF: 0.00404

Gnomad4 AMR AF: 0.0209

Gnomad4 ASJ AF: 0.0182

Gnomad4 EAS AF: 0.000580

Gnomad4 SAS AF: 0.0162

Gnomad4 FIN AF: 0.0147

Gnomad4 NFE AF: 0.0233

Gnomad4 OTH AF: 0.0118

Alfa AF: 0.0206 Hom.: 45

Bravo AF: 0.0160

Asia WGS AF: 0.00664 AC: 23 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.99
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: rs1459148; hg19: chr14-98840443;