rs10513333

Variant names:

• chr3-148586072-A-G
• rs10513333
• ENST00000648979.2:n.116+5746T>C

Your query was ambiguous. Multiple possible variants found:

• chr3-148586072-A-G
• chr3-148586072-A-T

Variant summary

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

The ENST00000648979.2(ENSG00000285557):​n.116+5746T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.335 in 152,054 control chromosomes in the GnomAD database, including 9,673 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 0.34 (9673 hom., cov: 31)
• Consequence: ENSG00000285557 ENST00000648979.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.197
• Publications: 5 publications found

Genes affected

ENSG00000285557 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.436 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000648979.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

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

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000285557	ENST00000648979.2		n.116+5746T>C		intron	N/A
	ENSG00000285557	ENST00000752703.1		n.118+5746T>C		intron	N/A
	ENSG00000285557	ENST00000752704.1		n.116+5746T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.335 AC: 50970 AN: 151938 Hom.: 9672 Cov.: 31

Gnomad AFR AF: 0.145

Gnomad AMI AF: 0.334

Gnomad AMR AF: 0.360

Gnomad ASJ AF: 0.396

Gnomad EAS AF: 0.281

Gnomad SAS AF: 0.339

Gnomad FIN AF: 0.378

Gnomad MID AF: 0.315

Gnomad NFE AF: 0.441

Gnomad OTH AF: 0.341

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

GnomAD4 genome AF: 0.335 AC: 50976 AN: 152054 Hom.: 9673 Cov.: 31 AF XY: 0.331 AC XY: 24626 AN XY: 74298

African (AFR) AF: 0.144 AC: 5991 AN: 41530

American (AMR) AF: 0.360 AC: 5489 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.396 AC: 1375 AN: 3472

East Asian (EAS) AF: 0.281 AC: 1449 AN: 5160

South Asian (SAS) AF: 0.340 AC: 1635 AN: 4814

European-Finnish (FIN) AF: 0.378 AC: 3981 AN: 10536

Middle Eastern (MID) AF: 0.312 AC: 91 AN: 292

European-Non Finnish (NFE) AF: 0.440 AC: 29936 AN: 67964

Other (OTH) AF: 0.343 AC: 725 AN: 2112

Alfa AF: 0.401 Hom.: 54547

Bravo AF: 0.324

Asia WGS AF: 0.305 AC: 1063 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	7.6
DANN	Benign	0.45
PhyloP100		0.20

Splicing

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

Other links and lift over

dbSNP: rs10513333; hg19: chr3-148303859;