rs1275288

Variant names:

• chr10-57300645-C-A
• rs1275288

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 0.591 in 151,990 control chromosomes in the GnomAD database, including 29,418 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 0.59 (29418 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.829
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.884 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: 0.590 AC: 89635 AN: 151870 Hom.: 29359 Cov.: 33

Gnomad AFR AF: 0.892

Gnomad AMI AF: 0.408

Gnomad AMR AF: 0.613

Gnomad ASJ AF: 0.459

Gnomad EAS AF: 0.300

Gnomad SAS AF: 0.577

Gnomad FIN AF: 0.459

Gnomad MID AF: 0.570

Gnomad NFE AF: 0.454

Gnomad OTH AF: 0.577

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

GnomAD4 genome AF: 0.591 AC: 89757 AN: 151990 Hom.: 29418 Cov.: 33 AF XY: 0.590 AC XY: 43796 AN XY: 74280

African (AFR) AF: 0.892 AC: 37031 AN: 41520

American (AMR) AF: 0.613 AC: 9366 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.459 AC: 1593 AN: 3468

East Asian (EAS) AF: 0.300 AC: 1549 AN: 5160

South Asian (SAS) AF: 0.577 AC: 2778 AN: 4816

European-Finnish (FIN) AF: 0.459 AC: 4834 AN: 10542

Middle Eastern (MID) AF: 0.588 AC: 173 AN: 294

European-Non Finnish (NFE) AF: 0.454 AC: 30857 AN: 67904

Other (OTH) AF: 0.572 AC: 1204 AN: 2104

Alfa AF: 0.534 Hom.: 3134

Bravo AF: 0.615

Asia WGS AF: 0.464 AC: 1604 AN: 3456

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.25
DANN	Benign	0.32
PhyloP100		-0.83

Splicing

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

Other links and lift over

dbSNP: rs1275288; hg19: chr10-59060405;