chr14-68796882-T-C

Variant names:

• chr14-68796882-T-C
• rs1465788

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 0.705 in 152,198 control chromosomes in the GnomAD database, including 37,946 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 0.70 (37946 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.198
• Publications: 79 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.746 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: 0.705 AC: 107200 AN: 152078 Hom.: 37921 Cov.: 33

Gnomad AFR AF: 0.668

Gnomad AMI AF: 0.704

Gnomad AMR AF: 0.718

Gnomad ASJ AF: 0.803

Gnomad EAS AF: 0.766

Gnomad SAS AF: 0.690

Gnomad FIN AF: 0.670

Gnomad MID AF: 0.794

Gnomad NFE AF: 0.720

Gnomad OTH AF: 0.720

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

GnomAD4 genome AF: 0.705 AC: 107275 AN: 152198 Hom.: 37946 Cov.: 33 AF XY: 0.703 AC XY: 52298 AN XY: 74388

African (AFR) AF: 0.668 AC: 27740 AN: 41510

American (AMR) AF: 0.718 AC: 10982 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.803 AC: 2787 AN: 3472

East Asian (EAS) AF: 0.765 AC: 3965 AN: 5180

South Asian (SAS) AF: 0.689 AC: 3319 AN: 4820

European-Finnish (FIN) AF: 0.670 AC: 7098 AN: 10600

Middle Eastern (MID) AF: 0.786 AC: 231 AN: 294

European-Non Finnish (NFE) AF: 0.720 AC: 48984 AN: 68012

Other (OTH) AF: 0.724 AC: 1527 AN: 2110

Alfa AF: 0.721 Hom.: 90569

Bravo AF: 0.709

Asia WGS AF: 0.728 AC: 2532 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	6.7
DANN	Benign	0.80
PhyloP100		-0.20

Splicing

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

Other links and lift over

dbSNP: rs1465788; hg19: chr14-69263599;