rs9615320

Variant names:

• chr22-48445115-G-A
• rs9615320

Your query was ambiguous. Multiple possible variants found:

• chr22-48445115-G-A
• chr22-48445115-G-T

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 0.103 in 152,230 control chromosomes in the GnomAD database, including 1,046 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 0.10 (1046 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.747
• Publications: 2 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.137 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: 0.103 AC: 15726 AN: 152112 Hom.: 1046 Cov.: 33

Gnomad AFR AF: 0.0263

Gnomad AMI AF: 0.102

Gnomad AMR AF: 0.116

Gnomad ASJ AF: 0.0862

Gnomad EAS AF: 0.0464

Gnomad SAS AF: 0.114

Gnomad FIN AF: 0.182

Gnomad MID AF: 0.130

Gnomad NFE AF: 0.139

Gnomad OTH AF: 0.111

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

GnomAD4 genome AF: 0.103 AC: 15717 AN: 152230 Hom.: 1046 Cov.: 33 AF XY: 0.107 AC XY: 7967 AN XY: 74428

African (AFR) AF: 0.0262 AC: 1090 AN: 41550

American (AMR) AF: 0.116 AC: 1780 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.0862 AC: 299 AN: 3470

East Asian (EAS) AF: 0.0458 AC: 237 AN: 5180

South Asian (SAS) AF: 0.114 AC: 548 AN: 4824

European-Finnish (FIN) AF: 0.182 AC: 1929 AN: 10590

Middle Eastern (MID) AF: 0.126 AC: 37 AN: 294

European-Non Finnish (NFE) AF: 0.139 AC: 9473 AN: 67994

Other (OTH) AF: 0.109 AC: 231 AN: 2116

Alfa AF: 0.0994 Hom.: 516

Bravo AF: 0.0935

Asia WGS AF: 0.0640 AC: 223 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.36
DANN	Benign	0.34
PhyloP100		-0.75

Splicing

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

Other links and lift over

dbSNP: rs9615320; hg19: chr22-48840927;