14-88370087-T-C

Variant names:

• chr14-88370087-T-C
• rs845766

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 0.94 in 152,238 control chromosomes in the GnomAD database, including 67,716 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 0.94 (67716 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.13
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.04).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.989 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: 0.940 AC: 143012 AN: 152120 Hom.: 67663 Cov.: 31

Gnomad AFR AF: 0.829

Gnomad AMI AF: 0.993

Gnomad AMR AF: 0.973

Gnomad ASJ AF: 0.998

Gnomad EAS AF: 0.904

Gnomad SAS AF: 0.864

Gnomad FIN AF: 0.999

Gnomad MID AF: 0.972

Gnomad NFE AF: 0.995

Gnomad OTH AF: 0.959

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

GnomAD4 genome AF: 0.940 AC: 143124 AN: 152238 Hom.: 67716 Cov.: 31 AF XY: 0.940 AC XY: 69928 AN XY: 74428

African (AFR) AF: 0.829 AC: 34429 AN: 41514

American (AMR) AF: 0.973 AC: 14877 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.998 AC: 3465 AN: 3472

East Asian (EAS) AF: 0.905 AC: 4680 AN: 5174

South Asian (SAS) AF: 0.864 AC: 4157 AN: 4810

European-Finnish (FIN) AF: 0.999 AC: 10615 AN: 10622

Middle Eastern (MID) AF: 0.973 AC: 286 AN: 294

European-Non Finnish (NFE) AF: 0.995 AC: 67681 AN: 68034

Other (OTH) AF: 0.959 AC: 2028 AN: 2114

Alfa AF: 0.965 Hom.: 8835

Bravo AF: 0.936

Asia WGS AF: 0.904 AC: 3145 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.84
DANN	Benign	0.31
PhyloP100		-2.1

Splicing

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

Other links and lift over

dbSNP: rs845766; hg19: chr14-88836431;