rs5412

Positions:

• chr17-7280727-G-A

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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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;