10-3305932-T-C

Variant names:

• chr10-3305932-T-C
• rs549676
• ENST00000783617.1:n.401-464A>G

Variant summary

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

The ENST00000783617.1(ENSG00000302051):​n.401-464A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.527 in 152,070 control chromosomes in the GnomAD database, including 21,510 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 0.53 (21510 hom., cov: 33)
• Consequence: ENSG00000302051 ENST00000783617.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.271
• Publications: 3 publications found

Genes affected

ENSG00000302051 (HGNC:):

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 = 0.633 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000783617.1. 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
	ENSG00000302051	ENST00000783617.1		n.401-464A>G		intron	N/A
	ENSG00000302051	ENST00000783618.1		n.401-464A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.527 AC: 80121 AN: 151952 Hom.: 21491 Cov.: 33

Gnomad AFR AF: 0.614

Gnomad AMI AF: 0.604

Gnomad AMR AF: 0.492

Gnomad ASJ AF: 0.531

Gnomad EAS AF: 0.651

Gnomad SAS AF: 0.518

Gnomad FIN AF: 0.422

Gnomad MID AF: 0.545

Gnomad NFE AF: 0.488

Gnomad OTH AF: 0.551

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

GnomAD4 genome AF: 0.527 AC: 80182 AN: 152070 Hom.: 21510 Cov.: 33 AF XY: 0.525 AC XY: 39041 AN XY: 74312

African (AFR) AF: 0.614 AC: 25437 AN: 41448

American (AMR) AF: 0.492 AC: 7517 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.531 AC: 1844 AN: 3470

East Asian (EAS) AF: 0.652 AC: 3376 AN: 5180

South Asian (SAS) AF: 0.517 AC: 2495 AN: 4822

European-Finnish (FIN) AF: 0.422 AC: 4461 AN: 10560

Middle Eastern (MID) AF: 0.558 AC: 163 AN: 292

European-Non Finnish (NFE) AF: 0.488 AC: 33177 AN: 67990

Other (OTH) AF: 0.549 AC: 1162 AN: 2116

Alfa AF: 0.502 Hom.: 53642

Bravo AF: 0.544

Asia WGS AF: 0.530 AC: 1841 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	4.9
DANN	Benign	0.47
PhyloP100		0.27

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs549676;

hg19: chr10-3348124;