5-56733416-T-C

Variant names:

• chr5-56733416-T-C
• rs16886181

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 0.175 in 152,040 control chromosomes in the GnomAD database, including 2,537 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 0.18 (2537 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.296
• Publications: 19 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.341 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: 0.175 AC: 26593 AN: 151922 Hom.: 2528 Cov.: 31

Gnomad AFR AF: 0.183

Gnomad AMI AF: 0.111

Gnomad AMR AF: 0.140

Gnomad ASJ AF: 0.170

Gnomad EAS AF: 0.354

Gnomad SAS AF: 0.330

Gnomad FIN AF: 0.135

Gnomad MID AF: 0.139

Gnomad NFE AF: 0.161

Gnomad OTH AF: 0.177

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

GnomAD4 genome AF: 0.175 AC: 26630 AN: 152040 Hom.: 2537 Cov.: 31 AF XY: 0.178 AC XY: 13222 AN XY: 74320

African (AFR) AF: 0.183 AC: 7603 AN: 41472

American (AMR) AF: 0.139 AC: 2132 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.170 AC: 590 AN: 3470

East Asian (EAS) AF: 0.355 AC: 1825 AN: 5144

South Asian (SAS) AF: 0.330 AC: 1587 AN: 4814

European-Finnish (FIN) AF: 0.135 AC: 1428 AN: 10586

Middle Eastern (MID) AF: 0.146 AC: 43 AN: 294

European-Non Finnish (NFE) AF: 0.161 AC: 10937 AN: 67950

Other (OTH) AF: 0.182 AC: 384 AN: 2112

Alfa AF: 0.168 Hom.: 5693

Bravo AF: 0.175

Asia WGS AF: 0.335 AC: 1162 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	6.7
DANN	Benign	0.80
PhyloP100		-0.30

Splicing

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

Other links and lift over

dbSNP: rs16886181; hg19: chr5-56029243;