rs1383279

chr8-49236274-A-Gchr8-49236274-A-T

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 0.847 in 152,134 control chromosomes in the GnomAD database, including 56,672 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 0.85 (56672 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.626

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.949 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: 0.847 AC: 128755 AN: 152016 Hom.: 56627 Cov.: 32

Gnomad AFR AF: 0.579

Gnomad AMI AF: 0.996

Gnomad AMR AF: 0.911

Gnomad ASJ AF: 0.968

Gnomad EAS AF: 0.962

Gnomad SAS AF: 0.971

Gnomad FIN AF: 0.963

Gnomad MID AF: 0.953

Gnomad NFE AF: 0.950

Gnomad OTH AF: 0.866

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

GnomAD4 genome AF: 0.847 AC: 128856 AN: 152134 Hom.: 56672 Cov.: 32 AF XY: 0.852 AC XY: 63345 AN XY: 74372

Gnomad4 AFR AF: 0.580

Gnomad4 AMR AF: 0.911

Gnomad4 ASJ AF: 0.968

Gnomad4 EAS AF: 0.962

Gnomad4 SAS AF: 0.972

Gnomad4 FIN AF: 0.963

Gnomad4 NFE AF: 0.950

Gnomad4 OTH AF: 0.868

Alfa AF: 0.881 Hom.: 7487

Bravo AF: 0.832

Asia WGS AF: 0.949 AC: 3298 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
Cadd	Benign	0.29
Dann	Benign	0.36

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1383279; hg19: chr8-50148833;