chr14-35415433-T-G

Variant names:

• chr14-35415433-T-G
• rs1012919

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 0.722 in 152,134 control chromosomes in the GnomAD database, including 39,918 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 0.72 (39918 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.324

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.795 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.722 AC: 109753 AN: 152016 Hom.: 39852 Cov.: 33

Gnomad AFR AF: 0.802

Gnomad AMI AF: 0.501

Gnomad AMR AF: 0.776

Gnomad ASJ AF: 0.702

Gnomad EAS AF: 0.738

Gnomad SAS AF: 0.732

Gnomad FIN AF: 0.728

Gnomad MID AF: 0.688

Gnomad NFE AF: 0.663

Gnomad OTH AF: 0.702

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

GnomAD4 genome AF: 0.722 AC: 109876 AN: 152134 Hom.: 39918 Cov.: 33 AF XY: 0.725 AC XY: 53901 AN XY: 74378

Gnomad4 AFR AF: 0.802

Gnomad4 AMR AF: 0.776

Gnomad4 ASJ AF: 0.702

Gnomad4 EAS AF: 0.739

Gnomad4 SAS AF: 0.732

Gnomad4 FIN AF: 0.728

Gnomad4 NFE AF: 0.663

Gnomad4 OTH AF: 0.705

Alfa AF: 0.677 Hom.: 70645

Bravo AF: 0.729

Asia WGS AF: 0.773 AC: 2686 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	5.4
DANN	Benign	0.60

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1012919; hg19: chr14-35884639;