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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC100128121		n.144517184G>A		intragenic_variant

Ensembl

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

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 v4.3

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;