5-151020289-A-G

Variant names:

• chr5-151020289-A-G
• rs8177409

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The variant allele was found at a frequency of 0.00000773 in 129,308 control chromosomes in the GnomAD database, with no homozygous occurrence. 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: not found (cov: 33)
  • Exomes 𝑓: 0.0000077 (0 hom.)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.220
• Publications: 0 publications found

ACMG classification

Our verdict: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes Cov.: 33

GnomAD4 exome AF: 0.00000773 AC: 1 AN: 129308 Hom.: 0 AF XY: 0.00 AC XY: 0 AN XY: 65574

African (AFR) AF: 0.00 AC: 0 AN: 4138

American (AMR) AF: 0.00 AC: 0 AN: 3536

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 5044

East Asian (EAS) AF: 0.00 AC: 0 AN: 9600

South Asian (SAS) AF: 0.00 AC: 0 AN: 4492

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 11018

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 708

European-Non Finnish (NFE) AF: 0.0000122 AC: 1 AN: 81894

Other (OTH) AF: 0.00 AC: 0 AN: 8878

GnomAD4 genome Cov.: 33

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	3.3
DANN	Benign	0.78
PhyloP100		-0.22
PromoterAI		0.0098	Neutral

Splicing

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

Other links and lift over

dbSNP: rs8177409; hg19: chr5-150399850;