rs9303621

Variant names:

• chr17-28834120-A-G
• rs9303621
• NM_001077498.3:c.-41+8562T>C

Your query was ambiguous. Multiple possible variants found:

• chr17-28834120-A-G
• chr17-28834120-A-T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001077498.3(FAM222B):​c.-41+8562T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.194 in 152,084 control chromosomes in the GnomAD database, including 2,970 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 0.19 (2970 hom., cov: 31)
• Consequence: FAM222B NM_001077498.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.328
• Publications: 10 publications found

Genes affected

FAM222B (HGNC:25563): (family with sequence similarity 222 member B) Located in nucleoplasm. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.283 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
FAM222B	NM_001077498.3	c.-41+8562T>C		intron_variant	Intron 1 of 2	ENST00000581407.6	NP_001070966.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
FAM222B	ENST00000581407.6	c.-41+8562T>C		intron_variant	Intron 1 of 2	1	NM_001077498.3	ENSP00000462419.1

Frequencies

GnomAD3 genomes AF: 0.194 AC: 29423 AN: 151966 Hom.: 2964 Cov.: 31

Gnomad AFR AF: 0.163

Gnomad AMI AF: 0.203

Gnomad AMR AF: 0.217

Gnomad ASJ AF: 0.229

Gnomad EAS AF: 0.192

Gnomad SAS AF: 0.297

Gnomad FIN AF: 0.188

Gnomad MID AF: 0.269

Gnomad NFE AF: 0.198

Gnomad OTH AF: 0.195

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

GnomAD4 genome AF: 0.194 AC: 29446 AN: 152084 Hom.: 2970 Cov.: 31 AF XY: 0.194 AC XY: 14409 AN XY: 74346

African (AFR) AF: 0.163 AC: 6769 AN: 41490

American (AMR) AF: 0.218 AC: 3327 AN: 15242

Ashkenazi Jewish (ASJ) AF: 0.229 AC: 794 AN: 3472

East Asian (EAS) AF: 0.193 AC: 996 AN: 5174

South Asian (SAS) AF: 0.296 AC: 1427 AN: 4824

European-Finnish (FIN) AF: 0.188 AC: 1986 AN: 10590

Middle Eastern (MID) AF: 0.265 AC: 78 AN: 294

European-Non Finnish (NFE) AF: 0.198 AC: 13473 AN: 67974

Other (OTH) AF: 0.194 AC: 411 AN: 2114

Alfa AF: 0.201 Hom.: 1790

Bravo AF: 0.193

Asia WGS AF: 0.245 AC: 855 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	7.3
DANN	Benign	0.64
PhyloP100		0.33
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Other links and lift over

dbSNP: rs9303621; hg19: chr17-27161138;