rs7350721

Variant names:

• chr14-55866795-A-G
• rs7350721
• ENST00000729158.1:n.492-1683A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000729158.1(ENSG00000259868):​n.492-1683A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.272 in 151,926 control chromosomes in the GnomAD database, including 6,997 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 0.27 (6997 hom., cov: 32)
• Consequence: ENSG00000259868 ENST00000729158.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.00200
• Publications: 6 publications found

Genes affected

ENSG00000259868 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.78).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.367 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
ENSG00000259868	ENST00000729158.1	n.492-1683A>G		intron_variant	Intron 2 of 8
ENSG00000259868	ENST00000729159.1	n.387-1683A>G		intron_variant	Intron 1 of 5
ENSG00000259868	ENST00000729160.1	n.387-1683A>G		intron_variant	Intron 1 of 4
ENSG00000259868	ENST00000729161.1	n.182-1683A>G		intron_variant	Intron 1 of 5

Frequencies

GnomAD3 genomes AF: 0.272 AC: 41268 AN: 151808 Hom.: 7001 Cov.: 32

Gnomad AFR AF: 0.0737

Gnomad AMI AF: 0.474

Gnomad AMR AF: 0.283

Gnomad ASJ AF: 0.372

Gnomad EAS AF: 0.267

Gnomad SAS AF: 0.275

Gnomad FIN AF: 0.338

Gnomad MID AF: 0.408

Gnomad NFE AF: 0.371

Gnomad OTH AF: 0.291

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

GnomAD4 genome AF: 0.272 AC: 41263 AN: 151926 Hom.: 6997 Cov.: 32 AF XY: 0.272 AC XY: 20165 AN XY: 74242

African (AFR) AF: 0.0734 AC: 3045 AN: 41462

American (AMR) AF: 0.283 AC: 4322 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.372 AC: 1293 AN: 3472

East Asian (EAS) AF: 0.266 AC: 1370 AN: 5152

South Asian (SAS) AF: 0.276 AC: 1326 AN: 4812

European-Finnish (FIN) AF: 0.338 AC: 3553 AN: 10512

Middle Eastern (MID) AF: 0.395 AC: 116 AN: 294

European-Non Finnish (NFE) AF: 0.371 AC: 25191 AN: 67930

Other (OTH) AF: 0.292 AC: 617 AN: 2112

Alfa AF: 0.300 Hom.: 1295

Bravo AF: 0.260

Asia WGS AF: 0.251 AC: 873 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
CADD	Benign	2.8
DANN	Benign	0.89
PhyloP100		0.0020

Splicing

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

Other links and lift over

dbSNP: rs7350721; hg19: chr14-56333513;