rs1547103

chr6-17209820-G-Achr6-17209820-G-T

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 0.337 in 152,012 control chromosomes in the GnomAD database, including 8,934 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 0.34 (8934 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.151

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.41 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.337 AC: 51213 AN: 151894 Hom.: 8903 Cov.: 32

Gnomad AFR AF: 0.396

Gnomad AMI AF: 0.298

Gnomad AMR AF: 0.380

Gnomad ASJ AF: 0.294

Gnomad EAS AF: 0.424

Gnomad SAS AF: 0.388

Gnomad FIN AF: 0.360

Gnomad MID AF: 0.272

Gnomad NFE AF: 0.282

Gnomad OTH AF: 0.319

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

GnomAD4 genome AF: 0.337 AC: 51292 AN: 152012 Hom.: 8934 Cov.: 32 AF XY: 0.342 AC XY: 25436 AN XY: 74286

Gnomad4 AFR AF: 0.396

Gnomad4 AMR AF: 0.380

Gnomad4 ASJ AF: 0.294

Gnomad4 EAS AF: 0.424

Gnomad4 SAS AF: 0.388

Gnomad4 FIN AF: 0.360

Gnomad4 NFE AF: 0.282

Gnomad4 OTH AF: 0.321

Alfa AF: 0.289 Hom.: 12115

Bravo AF: 0.340

Asia WGS AF: 0.349 AC: 1216 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	0.88
Dann	Benign	0.30

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1547103; hg19: chr6-17210051;