5-2364512-T-C

Variant names:

• chr5-2364512-T-C
• rs316598

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 0.471 in 152,076 control chromosomes in the GnomAD database, including 21,859 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 (21859 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.34
• Publications: 10 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.852 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: 0.471 AC: 71586 AN: 151956 Hom.: 21804 Cov.: 32

Gnomad AFR AF: 0.859

Gnomad AMI AF: 0.299

Gnomad AMR AF: 0.414

Gnomad ASJ AF: 0.417

Gnomad EAS AF: 0.592

Gnomad SAS AF: 0.473

Gnomad FIN AF: 0.300

Gnomad MID AF: 0.491

Gnomad NFE AF: 0.271

Gnomad OTH AF: 0.424

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

GnomAD4 genome AF: 0.471 AC: 71697 AN: 152076 Hom.: 21859 Cov.: 32 AF XY: 0.474 AC XY: 35261 AN XY: 74332

African (AFR) AF: 0.860 AC: 35699 AN: 41528

American (AMR) AF: 0.413 AC: 6308 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.417 AC: 1447 AN: 3470

East Asian (EAS) AF: 0.593 AC: 3044 AN: 5134

South Asian (SAS) AF: 0.471 AC: 2268 AN: 4816

European-Finnish (FIN) AF: 0.300 AC: 3176 AN: 10572

Middle Eastern (MID) AF: 0.500 AC: 147 AN: 294

European-Non Finnish (NFE) AF: 0.271 AC: 18431 AN: 67968

Other (OTH) AF: 0.430 AC: 904 AN: 2104

Alfa AF: 0.334 Hom.: 25267

Bravo AF: 0.498

Asia WGS AF: 0.542 AC: 1885 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.36
DANN	Benign	0.55
PhyloP100		-1.3

Splicing

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

Other links and lift over

dbSNP: rs316598; hg19: chr5-2364626;