14-42186072-A-G

Variant names:

• chr14-42186072-A-G
• rs2154294

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 0.554 in 151,726 control chromosomes in the GnomAD database, including 23,471 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 0.55 (23471 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.14
• Publications: 10 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.799 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.554 AC: 84008 AN: 151608 Hom.: 23450 Cov.: 31

Gnomad AFR AF: 0.557

Gnomad AMI AF: 0.455

Gnomad AMR AF: 0.549

Gnomad ASJ AF: 0.487

Gnomad EAS AF: 0.820

Gnomad SAS AF: 0.606

Gnomad FIN AF: 0.600

Gnomad MID AF: 0.576

Gnomad NFE AF: 0.527

Gnomad OTH AF: 0.543

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

GnomAD4 genome AF: 0.554 AC: 84072 AN: 151726 Hom.: 23471 Cov.: 31 AF XY: 0.562 AC XY: 41648 AN XY: 74134

African (AFR) AF: 0.557 AC: 23063 AN: 41404

American (AMR) AF: 0.549 AC: 8361 AN: 15226

Ashkenazi Jewish (ASJ) AF: 0.487 AC: 1686 AN: 3464

East Asian (EAS) AF: 0.820 AC: 4225 AN: 5152

South Asian (SAS) AF: 0.607 AC: 2923 AN: 4818

European-Finnish (FIN) AF: 0.600 AC: 6337 AN: 10560

Middle Eastern (MID) AF: 0.582 AC: 170 AN: 292

European-Non Finnish (NFE) AF: 0.527 AC: 35740 AN: 67798

Other (OTH) AF: 0.548 AC: 1155 AN: 2106

Alfa AF: 0.539 Hom.: 74238

Bravo AF: 0.544

Asia WGS AF: 0.680 AC: 2363 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	4.3
DANN	Benign	0.66
PhyloP100		2.1

Splicing

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

Other links and lift over

dbSNP: rs2154294; hg19: chr14-42655275;