5-92818872-T-C

Variant names:

• chr5-92818872-T-C
• rs17668565

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 0.459 in 152,048 control chromosomes in the GnomAD database, including 16,790 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 0.46 (16790 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.40
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.71).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.532 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: 0.459 AC: 69760 AN: 151930 Hom.: 16790 Cov.: 32

Gnomad AFR AF: 0.334

Gnomad AMI AF: 0.501

Gnomad AMR AF: 0.444

Gnomad ASJ AF: 0.514

Gnomad EAS AF: 0.252

Gnomad SAS AF: 0.410

Gnomad FIN AF: 0.576

Gnomad MID AF: 0.397

Gnomad NFE AF: 0.536

Gnomad OTH AF: 0.468

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

GnomAD4 genome AF: 0.459 AC: 69799 AN: 152048 Hom.: 16790 Cov.: 32 AF XY: 0.458 AC XY: 34059 AN XY: 74298

African (AFR) AF: 0.334 AC: 13867 AN: 41488

American (AMR) AF: 0.444 AC: 6777 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.514 AC: 1785 AN: 3472

East Asian (EAS) AF: 0.253 AC: 1303 AN: 5158

South Asian (SAS) AF: 0.410 AC: 1973 AN: 4816

European-Finnish (FIN) AF: 0.576 AC: 6091 AN: 10576

Middle Eastern (MID) AF: 0.403 AC: 117 AN: 290

European-Non Finnish (NFE) AF: 0.536 AC: 36440 AN: 67952

Other (OTH) AF: 0.468 AC: 991 AN: 2116

Alfa AF: 0.501 Hom.: 78617

Bravo AF: 0.444

Asia WGS AF: 0.344 AC: 1196 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.71
CADD	Benign	8.6
DANN	Benign	0.81
PhyloP100		1.4

Splicing

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

Other links and lift over

dbSNP: rs17668565; hg19: chr5-92154579; COSMIC: COSV60167821;