rs3851472

Variant names:

• chr5-127602219-T-C
• rs3851472

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

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

Gnomad4 AFR AF: 0.0865

Gnomad4 AMR AF: 0.0424

Gnomad4 ASJ AF: 0.0539

Gnomad4 EAS AF: 0.00598

Gnomad4 SAS AF: 0.0353

Gnomad4 FIN AF: 0.0683

Gnomad4 NFE AF: 0.0815

Gnomad4 OTH AF: 0.0607

Alfa AF: 0.0819 Hom.: 109

Bravo AF: 0.0710

Asia WGS AF: 0.0310 AC: 108 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3851472; hg19: chr5-126937911;