rs17568628

Variant names:

• chr5-76751114-T-C
• rs17568628

Your query was ambiguous. Multiple possible variants found:

• chr5-76751114-T-C
• chr5-76751114-T-G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The variant allele was found at a frequency of 0.026 in 152,294 control chromosomes in the GnomAD database, including 57 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 0.026 (57 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.03
• Publications: 19 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BS1: Variant frequency is greater than expected in population nfe. GnomAd4 allele frequency = 0.026 (3964/152294) while in subpopulation NFE AF = 0.0389 (2649/68012). AF 95% confidence interval is 0.0377. There are 57 homozygotes in GnomAd4. There are 1904 alleles in the male GnomAd4 subpopulation. Median coverage is 33. This position passed quality control check.
• BS2: High Homozygotes in GnomAd4 at 57 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.0260 AC: 3961 AN: 152176 Hom.: 57 Cov.: 33

Gnomad AFR AF: 0.00770

Gnomad AMI AF: 0.0757

Gnomad AMR AF: 0.0198

Gnomad ASJ AF: 0.0285

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00806

Gnomad FIN AF: 0.0400

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.0389

Gnomad OTH AF: 0.0282

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

GnomAD4 genome AF: 0.0260 AC: 3964 AN: 152294 Hom.: 57 Cov.: 33 AF XY: 0.0256 AC XY: 1904 AN XY: 74472

African (AFR) AF: 0.00767 AC: 319 AN: 41566

American (AMR) AF: 0.0198 AC: 303 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.0285 AC: 99 AN: 3468

East Asian (EAS) AF: 0.00 AC: 0 AN: 5188

South Asian (SAS) AF: 0.00849 AC: 41 AN: 4832

European-Finnish (FIN) AF: 0.0400 AC: 425 AN: 10616

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 294

European-Non Finnish (NFE) AF: 0.0389 AC: 2649 AN: 68012

Other (OTH) AF: 0.0279 AC: 59 AN: 2114

Alfa AF: 0.0320 Hom.: 227

Bravo AF: 0.0243

Asia WGS AF: 0.00375 AC: 13 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	5.5
DANN	Benign	0.87
PhyloP100		-1.0

Splicing

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

Other links and lift over

dbSNP: rs17568628; hg19: chr5-76046939;