5-165992501-T-C

Variant names:

• chr5-165992501-T-C
• rs1445716

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 0.473 in 151,620 control chromosomes in the GnomAD database, including 17,620 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 0.47 (17620 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.379
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.603 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.473 AC: 71686 AN: 151498 Hom.: 17616 Cov.: 30

Gnomad AFR AF: 0.610

Gnomad AMI AF: 0.333

Gnomad AMR AF: 0.335

Gnomad ASJ AF: 0.488

Gnomad EAS AF: 0.391

Gnomad SAS AF: 0.400

Gnomad FIN AF: 0.476

Gnomad MID AF: 0.519

Gnomad NFE AF: 0.434

Gnomad OTH AF: 0.446

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

GnomAD4 genome AF: 0.473 AC: 71719 AN: 151620 Hom.: 17620 Cov.: 30 AF XY: 0.471 AC XY: 34873 AN XY: 74068

African (AFR) AF: 0.610 AC: 25192 AN: 41330

American (AMR) AF: 0.334 AC: 5098 AN: 15246

Ashkenazi Jewish (ASJ) AF: 0.488 AC: 1690 AN: 3462

East Asian (EAS) AF: 0.390 AC: 1996 AN: 5122

South Asian (SAS) AF: 0.398 AC: 1907 AN: 4792

European-Finnish (FIN) AF: 0.476 AC: 4993 AN: 10498

Middle Eastern (MID) AF: 0.514 AC: 150 AN: 292

European-Non Finnish (NFE) AF: 0.434 AC: 29454 AN: 67864

Other (OTH) AF: 0.445 AC: 935 AN: 2102

Alfa AF: 0.445 Hom.: 57908

Bravo AF: 0.470

Asia WGS AF: 0.407 AC: 1417 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	2.8
DANN	Benign	0.46
PhyloP100		-0.38

Splicing

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

Other links and lift over

dbSNP: rs1445716; hg19: chr5-165419506;