rs11921014

chr3-141657298-C-A

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 0.0297 in 152,306 control chromosomes in the GnomAD database, including 93 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 0.030 (93 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.718

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BS1: Variant frequency is greater than expected in population nfe. gnomad4 allele frequency = 0.0297 (4520/152306) while in subpopulation NFE AF= 0.0435 (2957/68016). AF 95% confidence interval is 0.0422. There are 93 homozygotes in gnomad4. There are 2134 alleles in male gnomad4 subpopulation. Median coverage is 33. This position pass quality control queck.
• BS2: High Homozygotes in GnomAd at 93 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: 0.0297 AC: 4520 AN: 152188 Hom.: 93 Cov.: 33

Gnomad AFR AF: 0.0120

Gnomad AMI AF: 0.0340

Gnomad AMR AF: 0.0319

Gnomad ASJ AF: 0.0409

Gnomad EAS AF: 0.000193

Gnomad SAS AF: 0.0201

Gnomad FIN AF: 0.0199

Gnomad MID AF: 0.0791

Gnomad NFE AF: 0.0435

Gnomad OTH AF: 0.0340

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

GnomAD4 genome AF: 0.0297 AC: 4520 AN: 152306 Hom.: 93 Cov.: 33 AF XY: 0.0287 AC XY: 2134 AN XY: 74470

Gnomad4 AFR AF: 0.0120

Gnomad4 AMR AF: 0.0318

Gnomad4 ASJ AF: 0.0409

Gnomad4 EAS AF: 0.000193

Gnomad4 SAS AF: 0.0199

Gnomad4 FIN AF: 0.0199

Gnomad4 NFE AF: 0.0435

Gnomad4 OTH AF: 0.0336

Alfa AF: 0.0393 Hom.: 42

Bravo AF: 0.0306

Asia WGS AF: 0.0110 AC: 40 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
Cadd	Benign	0.96
Dann	Benign	0.27

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11921014; hg19: chr3-141376140;