chr7-54890765-G-A

Position:

• chr7-54890765-G-A

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 0.254 in 151,962 control chromosomes in the GnomAD database, including 5,351 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 0.25 (5351 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0500

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.307 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: 0.255 AC: 38675 AN: 151844 Hom.: 5353 Cov.: 33

Gnomad AFR AF: 0.203

Gnomad AMI AF: 0.442

Gnomad AMR AF: 0.225

Gnomad ASJ AF: 0.321

Gnomad EAS AF: 0.0199

Gnomad SAS AF: 0.177

Gnomad FIN AF: 0.243

Gnomad MID AF: 0.369

Gnomad NFE AF: 0.311

Gnomad OTH AF: 0.290

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

GnomAD4 genome AF: 0.254 AC: 38669 AN: 151962 Hom.: 5351 Cov.: 33 AF XY: 0.248 AC XY: 18394 AN XY: 74288

Gnomad4 AFR AF: 0.203

Gnomad4 AMR AF: 0.224

Gnomad4 ASJ AF: 0.321

Gnomad4 EAS AF: 0.0199

Gnomad4 SAS AF: 0.177

Gnomad4 FIN AF: 0.243

Gnomad4 NFE AF: 0.311

Gnomad4 OTH AF: 0.287

Alfa AF: 0.308 Hom.: 8884

Bravo AF: 0.251

Asia WGS AF: 0.0860 AC: 297 AN: 3436

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	5.1
DANN	Benign	0.25

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6945082; hg19: chr7-54958458;