rs7207449

Variant names:

• chr17-54542554-G-A
• rs7207449

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 0.203 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

ACMG classification

Verdict is Benign. Variant got -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.

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: 0.202 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

Gnomad4 AFR AF: 0.329

Gnomad4 AMR AF: 0.156

Gnomad4 ASJ AF: 0.239

Gnomad4 EAS AF: 0.0709

Gnomad4 SAS AF: 0.133

Gnomad4 FIN AF: 0.119

Gnomad4 NFE AF: 0.163

Gnomad4 OTH AF: 0.205

Alfa AF: 0.173 Hom.: 3321

Bravo AF: 0.212

Asia WGS AF: 0.126 AC: 440 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7207449; hg19: chr17-52619915;