14-102922443-A-T

Position:

• chr14-102922443-A-T

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_Strong BP6_Moderate BA1

The variant allele was found at a frequency of 0.457 in 152,028 control chromosomes in the GnomAD database, including 18,699 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency: Genomes: 𝑓 0.46 (18699 hom., cov: 31)
• Consequence: intergenic_region
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -2.62

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -14 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BP6: Variant 14-102922443-A-T is Benign according to our data. Variant chr14-102922443-A-T is described in ClinVar as [Benign]. Clinvar id is 1231371.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.735 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.102922443A>T		intergenic_region

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.456 AC: 69280 AN: 151910 Hom.: 18645 Cov.: 31

Gnomad AFR AF: 0.742

Gnomad AMI AF: 0.288

Gnomad AMR AF: 0.480

Gnomad ASJ AF: 0.331

Gnomad EAS AF: 0.583

Gnomad SAS AF: 0.355

Gnomad FIN AF: 0.365

Gnomad MID AF: 0.253

Gnomad NFE AF: 0.298

Gnomad OTH AF: 0.440

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

GnomAD4 genome AF: 0.457 AC: 69402 AN: 152028 Hom.: 18699 Cov.: 31 AF XY: 0.457 AC XY: 33961 AN XY: 74328

Gnomad4 AFR AF: 0.742

Gnomad4 AMR AF: 0.481

Gnomad4 ASJ AF: 0.331

Gnomad4 EAS AF: 0.584

Gnomad4 SAS AF: 0.353

Gnomad4 FIN AF: 0.365

Gnomad4 NFE AF: 0.298

Gnomad4 OTH AF: 0.442

Alfa AF: 0.393 Hom.: 1786

Bravo AF: 0.483

Asia WGS AF: 0.501 AC: 1738 AN: 3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Jul 07, 2018

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	0.13
DANN	Benign	0.64

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1211497; hg19: chr14-103388780;