chr5-174643623-G-A

Variant names:

• chr5-174643623-G-A
• rs6864839

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 0.271 in 151,496 control chromosomes in the GnomAD database, including 5,839 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 0.27 (5839 hom., cov: 29)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.752
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.311 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: 0.271 AC: 41067 AN: 151378 Hom.: 5838 Cov.: 29

Gnomad AFR AF: 0.185

Gnomad AMI AF: 0.284

Gnomad AMR AF: 0.256

Gnomad ASJ AF: 0.332

Gnomad EAS AF: 0.223

Gnomad SAS AF: 0.282

Gnomad FIN AF: 0.341

Gnomad MID AF: 0.361

Gnomad NFE AF: 0.315

Gnomad OTH AF: 0.292

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

GnomAD4 genome AF: 0.271 AC: 41082 AN: 151496 Hom.: 5839 Cov.: 29 AF XY: 0.273 AC XY: 20185 AN XY: 73964

African (AFR) AF: 0.185 AC: 7629 AN: 41286

American (AMR) AF: 0.255 AC: 3890 AN: 15232

Ashkenazi Jewish (ASJ) AF: 0.332 AC: 1150 AN: 3466

East Asian (EAS) AF: 0.223 AC: 1147 AN: 5136

South Asian (SAS) AF: 0.284 AC: 1361 AN: 4796

European-Finnish (FIN) AF: 0.341 AC: 3561 AN: 10434

Middle Eastern (MID) AF: 0.364 AC: 107 AN: 294

European-Non Finnish (NFE) AF: 0.315 AC: 21371 AN: 67854

Other (OTH) AF: 0.291 AC: 608 AN: 2090

Alfa AF: 0.300 Hom.: 901

Bravo AF: 0.260

Asia WGS AF: 0.289 AC: 1006 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	3.6
DANN	Benign	0.52
PhyloP100		0.75

Splicing

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

Other links and lift over

dbSNP: rs6864839; hg19: chr5-174070626;