rs7207449

Variant names:

• chr17-54542554-G-A
• rs7207449

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 0.203 in 151,984 control chromosomes in the GnomAD database, including 3,647 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 0.20 (3647 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.76
• Publications: 1 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.325 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: 0.202 AC: 30749 AN: 151864 Hom.: 3622 Cov.: 32

Gnomad AFR AF: 0.329

Gnomad AMI AF: 0.150

Gnomad AMR AF: 0.156

Gnomad ASJ AF: 0.239

Gnomad EAS AF: 0.0713

Gnomad SAS AF: 0.132

Gnomad FIN AF: 0.119

Gnomad MID AF: 0.247

Gnomad NFE AF: 0.163

Gnomad OTH AF: 0.207

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

GnomAD4 genome AF: 0.203 AC: 30808 AN: 151984 Hom.: 3647 Cov.: 32 AF XY: 0.198 AC XY: 14732 AN XY: 74332

African (AFR) AF: 0.329 AC: 13624 AN: 41388

American (AMR) AF: 0.156 AC: 2384 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.239 AC: 828 AN: 3464

East Asian (EAS) AF: 0.0709 AC: 367 AN: 5178

South Asian (SAS) AF: 0.133 AC: 644 AN: 4826

European-Finnish (FIN) AF: 0.119 AC: 1258 AN: 10594

Middle Eastern (MID) AF: 0.252 AC: 74 AN: 294

European-Non Finnish (NFE) AF: 0.163 AC: 11061 AN: 67956

Other (OTH) AF: 0.205 AC: 431 AN: 2104

Alfa AF: 0.178 Hom.: 4449

Bravo AF: 0.212

Asia WGS AF: 0.126 AC: 440 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	1.1
DANN	Benign	0.54
PhyloP100		-1.8

Splicing

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

Other links and lift over

dbSNP: rs7207449; hg19: chr17-52619915;