chr5-72409557-C-A

Variant names:

• chr5-72409557-C-A
• rs16878312

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 0.255 in 151,870 control chromosomes in the GnomAD database, including 5,163 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 0.25 (5163 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.75
• Publications: 6 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.314 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.255 AC: 38632 AN: 151750 Hom.: 5160 Cov.: 32

Gnomad AFR AF: 0.205

Gnomad AMI AF: 0.315

Gnomad AMR AF: 0.191

Gnomad ASJ AF: 0.281

Gnomad EAS AF: 0.0601

Gnomad SAS AF: 0.328

Gnomad FIN AF: 0.277

Gnomad MID AF: 0.253

Gnomad NFE AF: 0.303

Gnomad OTH AF: 0.251

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

GnomAD4 genome AF: 0.255 AC: 38654 AN: 151870 Hom.: 5163 Cov.: 32 AF XY: 0.253 AC XY: 18761 AN XY: 74190

African (AFR) AF: 0.205 AC: 8498 AN: 41428

American (AMR) AF: 0.191 AC: 2921 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.281 AC: 976 AN: 3468

East Asian (EAS) AF: 0.0604 AC: 312 AN: 5164

South Asian (SAS) AF: 0.327 AC: 1572 AN: 4802

European-Finnish (FIN) AF: 0.277 AC: 2907 AN: 10504

Middle Eastern (MID) AF: 0.252 AC: 74 AN: 294

European-Non Finnish (NFE) AF: 0.303 AC: 20585 AN: 67926

Other (OTH) AF: 0.247 AC: 522 AN: 2110

Alfa AF: 0.273 Hom.: 9371

Bravo AF: 0.239

Asia WGS AF: 0.189 AC: 656 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.14
DANN	Benign	0.31
PhyloP100		-1.8

Splicing

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

Other links and lift over

dbSNP: rs16878312; hg19: chr5-71705384;