rs224731

Variant names:

• chr10-33937381-G-A
• rs224731

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.751 in 152,042 control chromosomes in the GnomAD database, including 43,602 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 0.75 (43602 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.105

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.48).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.904 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: 0.751 AC: 114047 AN: 151924 Hom.: 43553 Cov.: 32

Gnomad AFR AF: 0.912

Gnomad AMI AF: 0.734

Gnomad AMR AF: 0.636

Gnomad ASJ AF: 0.644

Gnomad EAS AF: 0.756

Gnomad SAS AF: 0.754

Gnomad FIN AF: 0.695

Gnomad MID AF: 0.725

Gnomad NFE AF: 0.693

Gnomad OTH AF: 0.717

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

GnomAD4 genome AF: 0.751 AC: 114147 AN: 152042 Hom.: 43602 Cov.: 32 AF XY: 0.749 AC XY: 55616 AN XY: 74302

Gnomad4 AFR AF: 0.912

Gnomad4 AMR AF: 0.635

Gnomad4 ASJ AF: 0.644

Gnomad4 EAS AF: 0.756

Gnomad4 SAS AF: 0.753

Gnomad4 FIN AF: 0.695

Gnomad4 NFE AF: 0.693

Gnomad4 OTH AF: 0.715

Alfa AF: 0.700 Hom.: 47643

Bravo AF: 0.751

Asia WGS AF: 0.716 AC: 2490 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.48
CADD	Benign	5.2
DANN	Benign	0.80

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs224731; hg19: chr10-34226309;