rs5412

Variant names:

• chr17-7280727-G-A
• rs5412

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The variant allele was found at a frequency of 0.128 in 152,242 control chromosomes in the GnomAD database, including 1,664 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 0.13 (1664 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 3.81

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.45).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.225 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: 0.128 AC: 19482 AN: 152124 Hom.: 1662 Cov.: 32

Gnomad AFR AF: 0.0291

Gnomad AMI AF: 0.186

Gnomad AMR AF: 0.0896

Gnomad ASJ AF: 0.143

Gnomad EAS AF: 0.0570

Gnomad SAS AF: 0.236

Gnomad FIN AF: 0.269

Gnomad MID AF: 0.133

Gnomad NFE AF: 0.171

Gnomad OTH AF: 0.125

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

GnomAD4 genome AF: 0.128 AC: 19478 AN: 152242 Hom.: 1664 Cov.: 32 AF XY: 0.134 AC XY: 9983 AN XY: 74438

Gnomad4 AFR AF: 0.0290

Gnomad4 AMR AF: 0.0894

Gnomad4 ASJ AF: 0.143

Gnomad4 EAS AF: 0.0562

Gnomad4 SAS AF: 0.236

Gnomad4 FIN AF: 0.269

Gnomad4 NFE AF: 0.171

Gnomad4 OTH AF: 0.126

Alfa AF: 0.159 Hom.: 3051

Bravo AF: 0.105

Asia WGS AF: 0.135 AC: 470 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.45
CADD	Uncertain	24
DANN	Uncertain	0.99

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs5412; hg19: chr17-7184046; COSMIC: COSV58025969;