5-1297143-T-C

Variant names:

• chr5-1297143-T-C
• rs6554754

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 0.894 in 152,252 control chromosomes in the GnomAD database, including 61,017 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 0.89 (61017 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.653
• Publications: 5 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 = 0.945 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: 0.894 AC: 136017 AN: 152134 Hom.: 60951 Cov.: 32

Gnomad AFR AF: 0.953

Gnomad AMI AF: 0.882

Gnomad AMR AF: 0.895

Gnomad ASJ AF: 0.801

Gnomad EAS AF: 0.895

Gnomad SAS AF: 0.912

Gnomad FIN AF: 0.845

Gnomad MID AF: 0.775

Gnomad NFE AF: 0.871

Gnomad OTH AF: 0.862

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

GnomAD4 genome AF: 0.894 AC: 136142 AN: 152252 Hom.: 61017 Cov.: 32 AF XY: 0.893 AC XY: 66448 AN XY: 74414

African (AFR) AF: 0.952 AC: 39581 AN: 41558

American (AMR) AF: 0.895 AC: 13681 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.801 AC: 2780 AN: 3472

East Asian (EAS) AF: 0.895 AC: 4633 AN: 5174

South Asian (SAS) AF: 0.913 AC: 4400 AN: 4820

European-Finnish (FIN) AF: 0.845 AC: 8956 AN: 10602

Middle Eastern (MID) AF: 0.779 AC: 229 AN: 294

European-Non Finnish (NFE) AF: 0.871 AC: 59254 AN: 68020

Other (OTH) AF: 0.864 AC: 1824 AN: 2110

Alfa AF: 0.838 Hom.: 2595

Bravo AF: 0.900

Asia WGS AF: 0.920 AC: 3198 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	1.7
DANN	Benign	0.41
PhyloP100		-0.65

Splicing

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

Other links and lift over

dbSNP: rs6554754; hg19: chr5-1297258;