rs854549

chr7-95297273-C-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 0.26 in 152,136 control chromosomes in the GnomAD database, including 5,902 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 0.26 (5902 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.458

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.337 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: 0.260 AC: 39507 AN: 152016 Hom.: 5901 Cov.: 32

Gnomad AFR AF: 0.141

Gnomad AMI AF: 0.331

Gnomad AMR AF: 0.253

Gnomad ASJ AF: 0.408

Gnomad EAS AF: 0.0449

Gnomad SAS AF: 0.210

Gnomad FIN AF: 0.276

Gnomad MID AF: 0.458

Gnomad NFE AF: 0.341

Gnomad OTH AF: 0.301

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

GnomAD4 genome AF: 0.260 AC: 39512 AN: 152136 Hom.: 5902 Cov.: 32 AF XY: 0.254 AC XY: 18918 AN XY: 74358

Gnomad4 AFR AF: 0.141

Gnomad4 AMR AF: 0.252

Gnomad4 ASJ AF: 0.408

Gnomad4 EAS AF: 0.0452

Gnomad4 SAS AF: 0.212

Gnomad4 FIN AF: 0.276

Gnomad4 NFE AF: 0.341

Gnomad4 OTH AF: 0.298

Alfa AF: 0.329 Hom.: 8278

Bravo AF: 0.253

Asia WGS AF: 0.120 AC: 420 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
Cadd	Benign	2.5
Dann	Benign	0.69

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs854549; hg19: chr7-94926585;