rs17669975

Variant names:

• chr14-82838584-C-T
• rs17669975

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 0.107 in 151,976 control chromosomes in the GnomAD database, including 905 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 0.11 (905 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.386
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.142 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: 0.107 AC: 16251 AN: 151858 Hom.: 904 Cov.: 33

Gnomad AFR AF: 0.0803

Gnomad AMI AF: 0.0625

Gnomad AMR AF: 0.147

Gnomad ASJ AF: 0.127

Gnomad EAS AF: 0.0989

Gnomad SAS AF: 0.0971

Gnomad FIN AF: 0.123

Gnomad MID AF: 0.114

Gnomad NFE AF: 0.113

Gnomad OTH AF: 0.0946

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

GnomAD4 genome AF: 0.107 AC: 16266 AN: 151976 Hom.: 905 Cov.: 33 AF XY: 0.109 AC XY: 8097 AN XY: 74280

African (AFR) AF: 0.0803 AC: 3334 AN: 41504

American (AMR) AF: 0.147 AC: 2246 AN: 15232

Ashkenazi Jewish (ASJ) AF: 0.127 AC: 442 AN: 3470

East Asian (EAS) AF: 0.0993 AC: 513 AN: 5166

South Asian (SAS) AF: 0.0962 AC: 464 AN: 4824

European-Finnish (FIN) AF: 0.123 AC: 1298 AN: 10594

Middle Eastern (MID) AF: 0.122 AC: 36 AN: 294

European-Non Finnish (NFE) AF: 0.113 AC: 7676 AN: 67876

Other (OTH) AF: 0.0951 AC: 200 AN: 2104

Alfa AF: 0.110 Hom.: 256

Bravo AF: 0.106

Asia WGS AF: 0.0900 AC: 314 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	1.1
DANN	Benign	0.55
PhyloP100		-0.39

Splicing

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

Other links and lift over

dbSNP: rs17669975; hg19: chr14-83304928;