chr15-22835548-A-G

Variant names:

• chr15-22835548-A-G
• rs4778258

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 3 publications found

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.970 AC: 40244 AN: 41476

American (AMR) AF: 0.894 AC: 13659 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.843 AC: 2926 AN: 3472

East Asian (EAS) AF: 0.923 AC: 4756 AN: 5150

South Asian (SAS) AF: 0.920 AC: 4432 AN: 4816

European-Finnish (FIN) AF: 0.887 AC: 9350 AN: 10540

Middle Eastern (MID) AF: 0.878 AC: 258 AN: 294

European-Non Finnish (NFE) AF: 0.850 AC: 57812 AN: 67982

Other (OTH) AF: 0.884 AC: 1868 AN: 2112

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
PhyloP100		-0.48

Splicing

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

Other links and lift over

dbSNP: rs4778258; hg19: chr15-23037520;