rs1553850

Variant names:

• chr10-119179312-T-A
• rs1553850
• ENST00000826909.1:n.157+290T>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000826909.1(ENSG00000307533):​n.157+290T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. 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: ENSG00000307533 ENST00000826909.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.01
• Publications: 8 publications found

Genes affected

ENSG00000307533 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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
ENSG00000307533	ENST00000826909.1	n.157+290T>A		intron_variant	Intron 1 of 2
ENSG00000307533	ENST00000826910.1	n.136+290T>A		intron_variant	Intron 1 of 2
ENSG00000307533	ENST00000826911.1	n.56+290T>A		intron_variant	Intron 1 of 2

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

African (AFR) AF: 0.216 AC: 8963 AN: 41484

American (AMR) AF: 0.591 AC: 9030 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.563 AC: 1953 AN: 3466

East Asian (EAS) AF: 0.420 AC: 2170 AN: 5166

South Asian (SAS) AF: 0.581 AC: 2798 AN: 4818

European-Finnish (FIN) AF: 0.609 AC: 6447 AN: 10582

Middle Eastern (MID) AF: 0.486 AC: 143 AN: 294

European-Non Finnish (NFE) AF: 0.585 AC: 39772 AN: 67980

Other (OTH) AF: 0.517 AC: 1095 AN: 2116

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
PhyloP100		-2.0

Splicing

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

Other links and lift over

dbSNP: rs1553850; hg19: chr10-120938824;