chr5-127602219-T-C

Variant names:

• chr5-127602219-T-C
• rs3851472

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 0.0726 in 152,124 control chromosomes in the GnomAD database, including 419 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 0.073 (419 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0730
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0841 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: 0.0727 AC: 11047 AN: 152006 Hom.: 419 Cov.: 32

Gnomad AFR AF: 0.0868

Gnomad AMI AF: 0.0253

Gnomad AMR AF: 0.0425

Gnomad ASJ AF: 0.0539

Gnomad EAS AF: 0.00597

Gnomad SAS AF: 0.0349

Gnomad FIN AF: 0.0683

Gnomad MID AF: 0.0316

Gnomad NFE AF: 0.0815

Gnomad OTH AF: 0.0614

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

GnomAD4 genome AF: 0.0726 AC: 11047 AN: 152124 Hom.: 419 Cov.: 32 AF XY: 0.0696 AC XY: 5174 AN XY: 74382

African (AFR) AF: 0.0865 AC: 3585 AN: 41444

American (AMR) AF: 0.0424 AC: 649 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.0539 AC: 187 AN: 3470

East Asian (EAS) AF: 0.00598 AC: 31 AN: 5180

South Asian (SAS) AF: 0.0353 AC: 170 AN: 4816

European-Finnish (FIN) AF: 0.0683 AC: 724 AN: 10596

Middle Eastern (MID) AF: 0.0340 AC: 10 AN: 294

European-Non Finnish (NFE) AF: 0.0815 AC: 5540 AN: 68010

Other (OTH) AF: 0.0607 AC: 128 AN: 2108

Alfa AF: 0.0760 Hom.: 175

Bravo AF: 0.0710

Asia WGS AF: 0.0310 AC: 108 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	8.4
DANN	Benign	0.80
PhyloP100		0.073

Splicing

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

Other links and lift over

dbSNP: rs3851472; hg19: chr5-126937911;