chr14-102922602-C-G

Position:

• chr14-102922602-C-G

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_Strong BP6_Very_Strong BA1

The variant allele was found at a frequency of 0.115 in 1,493,412 control chromosomes in the GnomAD database, including 15,688 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

• Frequency:
  • Genomes: 𝑓 0.20 (5467 hom., cov: 32)
  • Exomes 𝑓: 0.11 (10221 hom.)
• Consequence: Unknown
• Clinical Significance: Benign criteria provided, multiple submitters, no conflicts B:2
• Conservation: PhyloP100: -1.04

ACMG classification

Verdict is Benign. Variant got -20 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BP6: Variant 14-102922602-C-G is Benign according to our data. Variant chr14-102922602-C-G is described in ClinVar as [Benign]. Clinvar id is 1286303.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.47 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.203 AC: 30883 AN: 151948 Hom.: 5442 Cov.: 32

Gnomad AFR AF: 0.475

Gnomad AMI AF: 0.185

Gnomad AMR AF: 0.137

Gnomad ASJ AF: 0.0936

Gnomad EAS AF: 0.00212

Gnomad SAS AF: 0.0736

Gnomad FIN AF: 0.0945

Gnomad MID AF: 0.120

Gnomad NFE AF: 0.102

Gnomad OTH AF: 0.170

GnomAD4 exome AF: 0.105 AC: 141322 AN: 1341346 Hom.: 10221 AF XY: 0.103 AC XY: 68396 AN XY: 661784

Gnomad4 AFR exome AF: 0.490

Gnomad4 AMR exome AF: 0.115

Gnomad4 ASJ exome AF: 0.0967

Gnomad4 EAS exome AF: 0.000901

Gnomad4 SAS exome AF: 0.0798

Gnomad4 FIN exome AF: 0.0940

Gnomad4 NFE exome AF: 0.0991

Gnomad4 OTH exome AF: 0.116

GnomAD4 genome AF: 0.204 AC: 30962 AN: 152066 Hom.: 5467 Cov.: 32 AF XY: 0.199 AC XY: 14776 AN XY: 74362

Gnomad4 AFR AF: 0.475

Gnomad4 AMR AF: 0.138

Gnomad4 ASJ AF: 0.0936

Gnomad4 EAS AF: 0.00193

Gnomad4 SAS AF: 0.0729

Gnomad4 FIN AF: 0.0945

Gnomad4 NFE AF: 0.102

Gnomad4 OTH AF: 0.169

Alfa AF: 0.0527 Hom.: 64

Bravo AF: 0.221

Asia WGS AF: 0.0700 AC: 245 AN: 3478

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

not provided Benign:2

Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -
Benign, criteria provided, single submitter	clinical testing	GeneDx	Oct 17, 2018	- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	3.7
DANN	Benign	0.75

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs59793431; hg19: chr14-103388939; COSMIC: COSV54486850;