rs114774257

Positions:

• chr3-146691396-T-C

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 0.015 in 152,184 control chromosomes in the GnomAD database, including 28 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 0.015 (28 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.214

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BS1: Variant frequency is greater than expected in population nfe. gnomad4 allele frequency = 0.015 (2276/152184) while in subpopulation NFE AF= 0.0244 (1660/67964). AF 95% confidence interval is 0.0234. There are 28 homozygotes in gnomad4. There are 1076 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
• BS2: High Homozygotes in GnomAd4 at 28 gene

Transcripts

RefSeq

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

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.0150 AC: 2276 AN: 152066 Hom.: 28 Cov.: 32

Gnomad AFR AF: 0.00490

Gnomad AMI AF: 0.00329

Gnomad AMR AF: 0.0157

Gnomad ASJ AF: 0.000289

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00683

Gnomad FIN AF: 0.00992

Gnomad MID AF: 0.00633

Gnomad NFE AF: 0.0244

Gnomad OTH AF: 0.0144

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

GnomAD4 genome AF: 0.0150 AC: 2276 AN: 152184 Hom.: 28 Cov.: 32 AF XY: 0.0145 AC XY: 1076 AN XY: 74410

Gnomad4 AFR AF: 0.00488

Gnomad4 AMR AF: 0.0156

Gnomad4 ASJ AF: 0.000289

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.00684

Gnomad4 FIN AF: 0.00992

Gnomad4 NFE AF: 0.0244

Gnomad4 OTH AF: 0.0142

Alfa AF: 0.0197 Hom.: 4

Bravo AF: 0.0147

Asia WGS AF: 0.00289 AC: 10 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	2.4
DANN	Benign	0.53

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs114774257; hg19: chr3-146409183;