5-1446604-C-G

Variant names:

• chr5-1446604-C-G
• rs2617596

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 0.46 in 151,534 control chromosomes in the GnomAD database, including 18,154 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 0.46 (18154 hom., cov: 29)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.00
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.591 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: 0.461 AC: 69741 AN: 151424 Hom.: 18143 Cov.: 29

Gnomad AFR AF: 0.239

Gnomad AMI AF: 0.530

Gnomad AMR AF: 0.468

Gnomad ASJ AF: 0.600

Gnomad EAS AF: 0.147

Gnomad SAS AF: 0.443

Gnomad FIN AF: 0.548

Gnomad MID AF: 0.557

Gnomad NFE AF: 0.596

Gnomad OTH AF: 0.491

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

GnomAD4 genome AF: 0.460 AC: 69775 AN: 151534 Hom.: 18154 Cov.: 29 AF XY: 0.458 AC XY: 33942 AN XY: 74054

African (AFR) AF: 0.238 AC: 9858 AN: 41372

American (AMR) AF: 0.468 AC: 7142 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.600 AC: 2078 AN: 3466

East Asian (EAS) AF: 0.147 AC: 757 AN: 5140

South Asian (SAS) AF: 0.445 AC: 2130 AN: 4786

European-Finnish (FIN) AF: 0.548 AC: 5747 AN: 10488

Middle Eastern (MID) AF: 0.562 AC: 164 AN: 292

European-Non Finnish (NFE) AF: 0.596 AC: 40386 AN: 67730

Other (OTH) AF: 0.493 AC: 1035 AN: 2098

Alfa AF: 0.332 Hom.: 759

Bravo AF: 0.440

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	3.3
DANN	Benign	0.22
PhyloP100		0.0

Splicing

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

Other links and lift over

dbSNP: rs2617596; hg19: chr5-1446719; COSMIC: COSV54362736;