rs9633289

Variant names:

• chr1-70639648-T-A
• rs9633289

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 0.0493 in 152,224 control chromosomes in the GnomAD database, including 325 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 0.049 (325 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.346
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.242 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: 0.0491 AC: 7470 AN: 152106 Hom.: 316 Cov.: 32

Gnomad AFR AF: 0.0463

Gnomad AMI AF: 0.00439

Gnomad AMR AF: 0.0751

Gnomad ASJ AF: 0.0409

Gnomad EAS AF: 0.252

Gnomad SAS AF: 0.118

Gnomad FIN AF: 0.0314

Gnomad MID AF: 0.0253

Gnomad NFE AF: 0.0287

Gnomad OTH AF: 0.0444

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

GnomAD4 genome AF: 0.0493 AC: 7507 AN: 152224 Hom.: 325 Cov.: 32 AF XY: 0.0522 AC XY: 3888 AN XY: 74420

African (AFR) AF: 0.0467 AC: 1941 AN: 41552

American (AMR) AF: 0.0758 AC: 1159 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.0409 AC: 142 AN: 3470

East Asian (EAS) AF: 0.253 AC: 1309 AN: 5176

South Asian (SAS) AF: 0.117 AC: 565 AN: 4820

European-Finnish (FIN) AF: 0.0314 AC: 333 AN: 10602

Middle Eastern (MID) AF: 0.0238 AC: 7 AN: 294

European-Non Finnish (NFE) AF: 0.0287 AC: 1951 AN: 68000

Other (OTH) AF: 0.0454 AC: 96 AN: 2116

Alfa AF: 0.0353 Hom.: 13

Bravo AF: 0.0533

Asia WGS AF: 0.159 AC: 552 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.1
DANN	Benign	0.67
PhyloP100		-0.35

Splicing

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

Other links and lift over

dbSNP: rs9633289; hg19: chr1-71105331;