15-22835548-A-G

Variant names:

• chr15-22835548-A-G
• rs4778258

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 0.895 in 152,024 control chromosomes in the GnomAD database, including 61,113 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 0.90 (61113 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.481

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.962 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: 0.895 AC: 135968 AN: 151906 Hom.: 61053 Cov.: 30

Gnomad AFR AF: 0.970

Gnomad AMI AF: 0.860

Gnomad AMR AF: 0.894

Gnomad ASJ AF: 0.843

Gnomad EAS AF: 0.924

Gnomad SAS AF: 0.921

Gnomad FIN AF: 0.887

Gnomad MID AF: 0.873

Gnomad NFE AF: 0.850

Gnomad OTH AF: 0.884

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

GnomAD4 genome AF: 0.895 AC: 136089 AN: 152024 Hom.: 61113 Cov.: 30 AF XY: 0.898 AC XY: 66678 AN XY: 74292

Gnomad4 AFR AF: 0.970

Gnomad4 AMR AF: 0.894

Gnomad4 ASJ AF: 0.843

Gnomad4 EAS AF: 0.923

Gnomad4 SAS AF: 0.920

Gnomad4 FIN AF: 0.887

Gnomad4 NFE AF: 0.850

Gnomad4 OTH AF: 0.884

Alfa AF: 0.846 Hom.: 5111

Bravo AF: 0.899

Asia WGS AF: 0.917 AC: 3185 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	2.5
DANN	Benign	0.72

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4778258; hg19: chr15-23037520;