rs454550

chr8-81279417-G-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The variant allele was found at a frequency of 0.0264 in 152,234 control chromosomes in the GnomAD database, including 72 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 0.026 (72 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.37

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BS1: Variant frequency is greater than expected in population nfe. gnomad4 allele frequency = 0.0264 (4017/152234) while in subpopulation NFE AF= 0.0387 (2634/68010). AF 95% confidence interval is 0.0375. There are 72 homozygotes in gnomad4. There are 1948 alleles in male gnomad4 subpopulation. Median coverage is 31. This position pass quality control queck.
• BS2: High Homozygotes in GnomAd at 72 gene

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: 0.0264 AC: 4016 AN: 152116 Hom.: 72 Cov.: 31

Gnomad AFR AF: 0.00715

Gnomad AMI AF: 0.0406

Gnomad AMR AF: 0.0376

Gnomad ASJ AF: 0.0516

Gnomad EAS AF: 0.000193

Gnomad SAS AF: 0.00871

Gnomad FIN AF: 0.0136

Gnomad MID AF: 0.0732

Gnomad NFE AF: 0.0388

Gnomad OTH AF: 0.0402

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

GnomAD4 genome AF: 0.0264 AC: 4017 AN: 152234 Hom.: 72 Cov.: 31 AF XY: 0.0262 AC XY: 1948 AN XY: 74442

Gnomad4 AFR AF: 0.00713

Gnomad4 AMR AF: 0.0374

Gnomad4 ASJ AF: 0.0516

Gnomad4 EAS AF: 0.000193

Gnomad4 SAS AF: 0.00913

Gnomad4 FIN AF: 0.0136

Gnomad4 NFE AF: 0.0387

Gnomad4 OTH AF: 0.0402

Alfa AF: 0.0310 Hom.: 9

Bravo AF: 0.0272

Asia WGS AF: 0.00260 AC: 9 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
Cadd	Benign	6.4
Dann	Benign	0.73

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs454550; hg19: chr8-82191652;