rs1553850

Variant names:

• chr10-119179312-T-A
• rs1553850

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 0.479 in 152,088 control chromosomes in the GnomAD database, including 19,728 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 0.48 (19728 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.01

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.581 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: 0.479 AC: 72843 AN: 151970 Hom.: 19724 Cov.: 32

Gnomad AFR AF: 0.216

Gnomad AMI AF: 0.545

Gnomad AMR AF: 0.591

Gnomad ASJ AF: 0.563

Gnomad EAS AF: 0.421

Gnomad SAS AF: 0.580

Gnomad FIN AF: 0.609

Gnomad MID AF: 0.500

Gnomad NFE AF: 0.585

Gnomad OTH AF: 0.517

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

GnomAD4 genome AF: 0.479 AC: 72868 AN: 152088 Hom.: 19728 Cov.: 32 AF XY: 0.485 AC XY: 36048 AN XY: 74366

Gnomad4 AFR AF: 0.216

Gnomad4 AMR AF: 0.591

Gnomad4 ASJ AF: 0.563

Gnomad4 EAS AF: 0.420

Gnomad4 SAS AF: 0.581

Gnomad4 FIN AF: 0.609

Gnomad4 NFE AF: 0.585

Gnomad4 OTH AF: 0.517

Alfa AF: 0.542 Hom.: 2991

Bravo AF: 0.463

Asia WGS AF: 0.524 AC: 1821 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.13
DANN	Benign	0.72

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1553850; hg19: chr10-120938824;