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. The variant received -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
• Publications: 3 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

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

African (AFR) AF: 0.396 AC: 16415 AN: 41448

American (AMR) AF: 0.380 AC: 5813 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.294 AC: 1019 AN: 3470

East Asian (EAS) AF: 0.424 AC: 2192 AN: 5166

South Asian (SAS) AF: 0.388 AC: 1870 AN: 4820

European-Finnish (FIN) AF: 0.360 AC: 3801 AN: 10546

Middle Eastern (MID) AF: 0.265 AC: 78 AN: 294

European-Non Finnish (NFE) AF: 0.282 AC: 19155 AN: 67970

Other (OTH) AF: 0.321 AC: 678 AN: 2110

Alfa AF: 0.298 Hom.: 20549

Bravo AF: 0.340

Asia WGS AF: 0.349 AC: 1216 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.88
DANN	Benign	0.30
PhyloP100		0.15

Splicing

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

Other links and lift over

dbSNP: rs1547103; hg19: chr6-17210051;