chr14-34897929-T-C

Variant names:

• chr14-34897929-T-C
• rs1200332

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 9 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.440 AC: 17469 AN: 39672

American (AMR) AF: 0.617 AC: 8901 AN: 14422

Ashkenazi Jewish (ASJ) AF: 0.807 AC: 2791 AN: 3458

East Asian (EAS) AF: 0.711 AC: 3539 AN: 4978

South Asian (SAS) AF: 0.733 AC: 3454 AN: 4714

European-Finnish (FIN) AF: 0.836 AC: 7409 AN: 8858

Middle Eastern (MID) AF: 0.689 AC: 193 AN: 280

European-Non Finnish (NFE) AF: 0.788 AC: 53169 AN: 67506

Other (OTH) AF: 0.668 AC: 1360 AN: 2036

Alfa AF: 0.763 Hom.: 68535

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
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs1200332; hg19: chr14-35367135;