rs17738966

Variant names:

• chr14-54835501-G-A
• rs17738966

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 0.0879 in 152,224 control chromosomes in the GnomAD database, including 923 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 0.088 (923 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.05
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.123 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: 0.0880 AC: 13390 AN: 152106 Hom.: 924 Cov.: 32

Gnomad AFR AF: 0.0190

Gnomad AMI AF: 0.180

Gnomad AMR AF: 0.0661

Gnomad ASJ AF: 0.0490

Gnomad EAS AF: 0.00269

Gnomad SAS AF: 0.0671

Gnomad FIN AF: 0.212

Gnomad MID AF: 0.0253

Gnomad NFE AF: 0.125

Gnomad OTH AF: 0.0770

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

GnomAD4 genome AF: 0.0879 AC: 13387 AN: 152224 Hom.: 923 Cov.: 32 AF XY: 0.0908 AC XY: 6760 AN XY: 74420

African (AFR) AF: 0.0190 AC: 789 AN: 41562

American (AMR) AF: 0.0660 AC: 1009 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.0490 AC: 170 AN: 3466

East Asian (EAS) AF: 0.00270 AC: 14 AN: 5186

South Asian (SAS) AF: 0.0667 AC: 322 AN: 4828

European-Finnish (FIN) AF: 0.212 AC: 2239 AN: 10556

Middle Eastern (MID) AF: 0.0272 AC: 8 AN: 294

European-Non Finnish (NFE) AF: 0.125 AC: 8511 AN: 68012

Other (OTH) AF: 0.0762 AC: 161 AN: 2114

Alfa AF: 0.115 Hom.: 630

Bravo AF: 0.0723

Asia WGS AF: 0.0330 AC: 116 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.012
DANN	Benign	0.72
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs17738966; hg19: chr14-55302219;