10-33137219-T-C

Variant names:

• chr10-33137219-T-C
• rs722988

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 0.44 in 152,002 control chromosomes in the GnomAD database, including 15,481 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 0.44 (15481 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.508
• Publications: 17 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.732 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.440 AC: 66791 AN: 151884 Hom.: 15476 Cov.: 32

Gnomad AFR AF: 0.530

Gnomad AMI AF: 0.309

Gnomad AMR AF: 0.454

Gnomad ASJ AF: 0.462

Gnomad EAS AF: 0.753

Gnomad SAS AF: 0.542

Gnomad FIN AF: 0.308

Gnomad MID AF: 0.363

Gnomad NFE AF: 0.371

Gnomad OTH AF: 0.471

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

GnomAD4 genome AF: 0.440 AC: 66833 AN: 152002 Hom.: 15481 Cov.: 32 AF XY: 0.439 AC XY: 32588 AN XY: 74280

African (AFR) AF: 0.530 AC: 21959 AN: 41458

American (AMR) AF: 0.454 AC: 6934 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.462 AC: 1598 AN: 3460

East Asian (EAS) AF: 0.752 AC: 3886 AN: 5166

South Asian (SAS) AF: 0.542 AC: 2614 AN: 4820

European-Finnish (FIN) AF: 0.308 AC: 3250 AN: 10552

Middle Eastern (MID) AF: 0.370 AC: 108 AN: 292

European-Non Finnish (NFE) AF: 0.371 AC: 25214 AN: 67956

Other (OTH) AF: 0.470 AC: 989 AN: 2106

Alfa AF: 0.399 Hom.: 54404

Bravo AF: 0.452

Asia WGS AF: 0.626 AC: 2180 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.87
DANN	Benign	0.36
PhyloP100		-0.51

Splicing

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

Other links and lift over

dbSNP: rs722988; hg19: chr10-33426147;