chr5-166401303-A-T

Variant names:

• chr5-166401303-A-T
• rs17384913

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 0.135 in 133,034 control chromosomes in the GnomAD database, including 1,448 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 0.14 (1448 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.160
• Publications: 0 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.23 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: 0.136 AC: 18014 AN: 132914 Hom.: 1451 Cov.: 30

Gnomad AFR AF: 0.0360

Gnomad AMI AF: 0.355

Gnomad AMR AF: 0.150

Gnomad ASJ AF: 0.248

Gnomad EAS AF: 0.185

Gnomad SAS AF: 0.242

Gnomad FIN AF: 0.104

Gnomad MID AF: 0.229

Gnomad NFE AF: 0.174

Gnomad OTH AF: 0.168

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

GnomAD4 genome AF: 0.135 AC: 18006 AN: 133034 Hom.: 1448 Cov.: 30 AF XY: 0.134 AC XY: 8635 AN XY: 64650

African (AFR) AF: 0.0359 AC: 1281 AN: 35650

American (AMR) AF: 0.150 AC: 1930 AN: 12872

Ashkenazi Jewish (ASJ) AF: 0.248 AC: 800 AN: 3228

East Asian (EAS) AF: 0.185 AC: 800 AN: 4316

South Asian (SAS) AF: 0.242 AC: 1040 AN: 4302

European-Finnish (FIN) AF: 0.104 AC: 961 AN: 9208

Middle Eastern (MID) AF: 0.232 AC: 57 AN: 246

European-Non Finnish (NFE) AF: 0.174 AC: 10539 AN: 60538

Other (OTH) AF: 0.164 AC: 303 AN: 1844

Alfa AF: 0.0617 Hom.: 75

Bravo AF: 0.118

Asia WGS AF: 0.168 AC: 586 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	1.1
DANN	Benign	0.78
PhyloP100		-0.16

Splicing

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

Other links and lift over

dbSNP: rs17384913; hg19: chr5-165828308;