rs1547103

Variant names:

• chr6-17209820-G-A
• rs1547103

Your query was ambiguous. Multiple possible variants found:

• chr6-17209820-G-A
• chr6-17209820-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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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;