14-85343567-T-C

Variant names:

• chr14-85343567-T-C
• rs17796783

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 0.232 in 152,172 control chromosomes in the GnomAD database, including 4,362 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 0.23 (4362 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.764
• Publications: 17 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.28 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.232 AC: 35283 AN: 152056 Hom.: 4352 Cov.: 33

Gnomad AFR AF: 0.163

Gnomad AMI AF: 0.276

Gnomad AMR AF: 0.228

Gnomad ASJ AF: 0.279

Gnomad EAS AF: 0.118

Gnomad SAS AF: 0.203

Gnomad FIN AF: 0.224

Gnomad MID AF: 0.244

Gnomad NFE AF: 0.284

Gnomad OTH AF: 0.253

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

GnomAD4 genome AF: 0.232 AC: 35321 AN: 152172 Hom.: 4362 Cov.: 33 AF XY: 0.228 AC XY: 16925 AN XY: 74382

African (AFR) AF: 0.163 AC: 6764 AN: 41528

American (AMR) AF: 0.228 AC: 3485 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.279 AC: 969 AN: 3468

East Asian (EAS) AF: 0.118 AC: 613 AN: 5176

South Asian (SAS) AF: 0.204 AC: 983 AN: 4824

European-Finnish (FIN) AF: 0.224 AC: 2366 AN: 10578

Middle Eastern (MID) AF: 0.245 AC: 72 AN: 294

European-Non Finnish (NFE) AF: 0.284 AC: 19284 AN: 67988

Other (OTH) AF: 0.253 AC: 534 AN: 2112

Alfa AF: 0.270 Hom.: 24315

Bravo AF: 0.231

Asia WGS AF: 0.173 AC: 601 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	2.4
DANN	Benign	0.73
PhyloP100		-0.76

Splicing

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

Other links and lift over

dbSNP: rs17796783; hg19: chr14-85809911;