rs1200332

chr14-34897929-T-Cchr14-34897929-T-G

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 0.674 in 146,824 control chromosomes in the GnomAD database, including 35,045 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 0.67 (35045 hom., cov: 25)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.08

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.04).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.782 is higher than 0.05.

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: 0.674 AC: 98872 AN: 146732 Hom.: 35048 Cov.: 25

Gnomad AFR AF: 0.440

Gnomad AMI AF: 0.678

Gnomad AMR AF: 0.618

Gnomad ASJ AF: 0.807

Gnomad EAS AF: 0.711

Gnomad SAS AF: 0.733

Gnomad FIN AF: 0.836

Gnomad MID AF: 0.684

Gnomad NFE AF: 0.788

Gnomad OTH AF: 0.669

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

GnomAD4 genome AF: 0.674 AC: 98895 AN: 146824 Hom.: 35045 Cov.: 25 AF XY: 0.674 AC XY: 47937 AN XY: 71116

Gnomad4 AFR AF: 0.440

Gnomad4 AMR AF: 0.617

Gnomad4 ASJ AF: 0.807

Gnomad4 EAS AF: 0.711

Gnomad4 SAS AF: 0.733

Gnomad4 FIN AF: 0.836

Gnomad4 NFE AF: 0.788

Gnomad4 OTH AF: 0.668

Alfa AF: 0.767 Hom.: 58009

Bravo AF: 0.648

Asia WGS AF: 0.674 AC: 2343 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	1.3
Dann	Benign	0.39

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1200332; hg19: chr14-35367135;