rs28362317

Variant names:

• chr5-1447729-T-A
• rs28362317

Your query was ambiguous. Multiple possible variants found:

• chr5-1447729-T-A
• chr5-1447729-T-G

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 0.0508 in 152,258 control chromosomes in the GnomAD database, including 305 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 0.051 (305 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.264
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0757 is higher than 0.05.

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: 0.0508 AC: 7728 AN: 152140 Hom.: 305 Cov.: 33

Gnomad AFR AF: 0.0126

Gnomad AMI AF: 0.0888

Gnomad AMR AF: 0.0221

Gnomad ASJ AF: 0.0144

Gnomad EAS AF: 0.000578

Gnomad SAS AF: 0.00621

Gnomad FIN AF: 0.129

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.0774

Gnomad OTH AF: 0.0335

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

GnomAD4 genome AF: 0.0508 AC: 7729 AN: 152258 Hom.: 305 Cov.: 33 AF XY: 0.0508 AC XY: 3780 AN XY: 74450

African (AFR) AF: 0.0126 AC: 522 AN: 41566

American (AMR) AF: 0.0220 AC: 337 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.0144 AC: 50 AN: 3468

East Asian (EAS) AF: 0.000579 AC: 3 AN: 5178

South Asian (SAS) AF: 0.00642 AC: 31 AN: 4830

European-Finnish (FIN) AF: 0.129 AC: 1373 AN: 10608

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

European-Non Finnish (NFE) AF: 0.0774 AC: 5263 AN: 67992

Other (OTH) AF: 0.0326 AC: 69 AN: 2114

Alfa AF: 0.0363 Hom.: 21

Bravo AF: 0.0424

Asia WGS AF: 0.00635 AC: 22 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	0.94
DANN	Benign	0.41
PhyloP100		0.26

Splicing

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

Other links and lift over

dbSNP: rs28362317; hg19: chr5-1447844;