rs2288335

Variant names:

• chr10-52319294-G-A
• rs2288335

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 0.0751 in 152,158 control chromosomes in the GnomAD database, including 476 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 0.075 (476 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.208
• Publications: 8 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.133 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: 0.0751 AC: 11412 AN: 152040 Hom.: 474 Cov.: 32

Gnomad AFR AF: 0.0816

Gnomad AMI AF: 0.170

Gnomad AMR AF: 0.0606

Gnomad ASJ AF: 0.0423

Gnomad EAS AF: 0.0874

Gnomad SAS AF: 0.142

Gnomad FIN AF: 0.0373

Gnomad MID AF: 0.0823

Gnomad NFE AF: 0.0750

Gnomad OTH AF: 0.0703

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

GnomAD4 genome AF: 0.0751 AC: 11423 AN: 152158 Hom.: 476 Cov.: 32 AF XY: 0.0746 AC XY: 5551 AN XY: 74390

African (AFR) AF: 0.0816 AC: 3387 AN: 41530

American (AMR) AF: 0.0606 AC: 925 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.0423 AC: 147 AN: 3472

East Asian (EAS) AF: 0.0874 AC: 451 AN: 5162

South Asian (SAS) AF: 0.142 AC: 684 AN: 4816

European-Finnish (FIN) AF: 0.0373 AC: 395 AN: 10596

Middle Eastern (MID) AF: 0.0850 AC: 25 AN: 294

European-Non Finnish (NFE) AF: 0.0750 AC: 5101 AN: 67990

Other (OTH) AF: 0.0724 AC: 153 AN: 2112

Alfa AF: 0.0751 Hom.: 747

Bravo AF: 0.0748

Asia WGS AF: 0.143 AC: 498 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	4.0
DANN	Benign	0.60
PhyloP100		0.21

Splicing

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

Other links and lift over

dbSNP: rs2288335; hg19: chr10-54079054;