rs165519

Variant names:

• chr5-144517184-G-A
• rs165519

Your query was ambiguous. Multiple possible variants found:

• chr5-144517184-G-A
• chr5-144517184-G-C

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 0.455 in 151,728 control chromosomes in the GnomAD database, including 16,034 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 (16034 hom., cov: 32)
• Consequence: LOC100128121 intragenic
• Clinical Significance: Not reported in ClinVar
• Conservation: No conservation score assigned
• Publications: 1 publications found

Genes affected

LOC100128121 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.59 is higher than 0.05.

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 AF: 0.455 AC: 69000 AN: 151610 Hom.: 15997 Cov.: 32

Gnomad AFR AF: 0.517

Gnomad AMI AF: 0.475

Gnomad AMR AF: 0.513

Gnomad ASJ AF: 0.500

Gnomad EAS AF: 0.608

Gnomad SAS AF: 0.400

Gnomad FIN AF: 0.383

Gnomad MID AF: 0.380

Gnomad NFE AF: 0.407

Gnomad OTH AF: 0.431

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

GnomAD4 genome AF: 0.455 AC: 69089 AN: 151728 Hom.: 16034 Cov.: 32 AF XY: 0.456 AC XY: 33787 AN XY: 74150

African (AFR) AF: 0.517 AC: 21356 AN: 41314

American (AMR) AF: 0.513 AC: 7833 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.500 AC: 1732 AN: 3466

East Asian (EAS) AF: 0.608 AC: 3132 AN: 5152

South Asian (SAS) AF: 0.401 AC: 1927 AN: 4810

European-Finnish (FIN) AF: 0.383 AC: 4032 AN: 10540

Middle Eastern (MID) AF: 0.388 AC: 114 AN: 294

European-Non Finnish (NFE) AF: 0.407 AC: 27613 AN: 67876

Other (OTH) AF: 0.436 AC: 917 AN: 2104

Alfa AF: 0.446 Hom.: 1899

Bravo AF: 0.469

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.39
DANN	Benign	0.81

Splicing

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

Other links and lift over

dbSNP: rs165519; hg19: chr5-143896747; COSMIC: COSV73634704;