14-48058363-T-C

Variant names:

• chr14-48058363-T-C
• rs698322

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 0.286 in 152,040 control chromosomes in the GnomAD database, including 7,235 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 0.29 (7235 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.647
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.473 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: 0.286 AC: 43489 AN: 151922 Hom.: 7235 Cov.: 32

Gnomad AFR AF: 0.120

Gnomad AMI AF: 0.176

Gnomad AMR AF: 0.411

Gnomad ASJ AF: 0.292

Gnomad EAS AF: 0.329

Gnomad SAS AF: 0.491

Gnomad FIN AF: 0.303

Gnomad MID AF: 0.237

Gnomad NFE AF: 0.340

Gnomad OTH AF: 0.314

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

GnomAD4 genome AF: 0.286 AC: 43487 AN: 152040 Hom.: 7235 Cov.: 32 AF XY: 0.288 AC XY: 21421 AN XY: 74312

African (AFR) AF: 0.119 AC: 4952 AN: 41534

American (AMR) AF: 0.411 AC: 6276 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.292 AC: 1013 AN: 3472

East Asian (EAS) AF: 0.329 AC: 1699 AN: 5158

South Asian (SAS) AF: 0.489 AC: 2352 AN: 4806

European-Finnish (FIN) AF: 0.303 AC: 3209 AN: 10576

Middle Eastern (MID) AF: 0.235 AC: 69 AN: 294

European-Non Finnish (NFE) AF: 0.340 AC: 23099 AN: 67922

Other (OTH) AF: 0.312 AC: 658 AN: 2110

Alfa AF: 0.323 Hom.: 11032

Bravo AF: 0.284

Asia WGS AF: 0.381 AC: 1320 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.6
DANN	Benign	0.52
PhyloP100		0.65

Splicing

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

Other links and lift over

dbSNP: rs698322; hg19: chr14-48527566;