14-99141143-A-G

Variant names:

• chr14-99141143-A-G
• rs2693676

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 0.26 in 151,806 control chromosomes in the GnomAD database, including 6,368 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 0.26 (6368 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.10
• Publications: 7 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.437 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: 0.260 AC: 39378 AN: 151688 Hom.: 6364 Cov.: 31

Gnomad AFR AF: 0.443

Gnomad AMI AF: 0.145

Gnomad AMR AF: 0.315

Gnomad ASJ AF: 0.143

Gnomad EAS AF: 0.325

Gnomad SAS AF: 0.330

Gnomad FIN AF: 0.140

Gnomad MID AF: 0.244

Gnomad NFE AF: 0.153

Gnomad OTH AF: 0.231

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

GnomAD4 genome AF: 0.260 AC: 39406 AN: 151806 Hom.: 6368 Cov.: 31 AF XY: 0.262 AC XY: 19423 AN XY: 74192

African (AFR) AF: 0.442 AC: 18279 AN: 41348

American (AMR) AF: 0.316 AC: 4814 AN: 15252

Ashkenazi Jewish (ASJ) AF: 0.143 AC: 495 AN: 3470

East Asian (EAS) AF: 0.325 AC: 1663 AN: 5114

South Asian (SAS) AF: 0.330 AC: 1586 AN: 4804

European-Finnish (FIN) AF: 0.140 AC: 1475 AN: 10564

Middle Eastern (MID) AF: 0.241 AC: 71 AN: 294

European-Non Finnish (NFE) AF: 0.153 AC: 10408 AN: 67946

Other (OTH) AF: 0.230 AC: 484 AN: 2108

Alfa AF: 0.297 Hom.: 3031

Bravo AF: 0.281

Asia WGS AF: 0.335 AC: 1168 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.10
DANN	Benign	0.43
PhyloP100		-3.1

Splicing

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

Other links and lift over

dbSNP: rs2693676; hg19: chr14-99607480;