rs721909

Positions:

• chr14-100863466-G-A
• chr14-100863466-G-T

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 0.159 in 151,402 control chromosomes in the GnomAD database, including 2,475 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 0.16 (2475 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.46

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.265 is higher than 0.05.

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: 0.159 AC: 24093 AN: 151278 Hom.: 2473 Cov.: 33

Gnomad AFR AF: 0.0407

Gnomad AMI AF: 0.180

Gnomad AMR AF: 0.272

Gnomad ASJ AF: 0.258

Gnomad EAS AF: 0.153

Gnomad SAS AF: 0.0658

Gnomad FIN AF: 0.122

Gnomad MID AF: 0.268

Gnomad NFE AF: 0.212

Gnomad OTH AF: 0.201

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

GnomAD4 genome AF: 0.159 AC: 24110 AN: 151402 Hom.: 2475 Cov.: 33 AF XY: 0.155 AC XY: 11480 AN XY: 73968

Gnomad4 AFR AF: 0.0406

Gnomad4 AMR AF: 0.272

Gnomad4 ASJ AF: 0.258

Gnomad4 EAS AF: 0.153

Gnomad4 SAS AF: 0.0665

Gnomad4 FIN AF: 0.122

Gnomad4 NFE AF: 0.212

Gnomad4 OTH AF: 0.202

Alfa AF: 0.139 Hom.: 398

Bravo AF: 0.168

Asia WGS AF: 0.128 AC: 448 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.044
DANN	Benign	0.70

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs721909; hg19: chr14-101329803;