rs1325586

Variant names:

• chr10-3281581-T-C
• rs1325586
• ENST00000724949.1:n.109+4488T>C

Variant summary

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

The ENST00000724949.1(ENSG00000294649):​n.109+4488T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.6 in 152,142 control chromosomes in the GnomAD database, including 27,568 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 0.60 (27568 hom., cov: 34)
• Consequence: ENSG00000294649 ENST00000724949.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.572
• Publications: 3 publications found

Genes affected

ENSG00000294649 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.71 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000724949.1. 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
	ENSG00000294649	ENST00000724949.1		n.109+4488T>C		intron	N/A
	ENSG00000294649	ENST00000724950.1		n.385+4488T>C		intron	N/A
	ENSG00000294649	ENST00000724951.1		n.35+4488T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.600 AC: 91154 AN: 152024 Hom.: 27552 Cov.: 34

Gnomad AFR AF: 0.575

Gnomad AMI AF: 0.605

Gnomad AMR AF: 0.698

Gnomad ASJ AF: 0.468

Gnomad EAS AF: 0.504

Gnomad SAS AF: 0.730

Gnomad FIN AF: 0.600

Gnomad MID AF: 0.510

Gnomad NFE AF: 0.597

Gnomad OTH AF: 0.602

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

GnomAD4 genome AF: 0.600 AC: 91210 AN: 152142 Hom.: 27568 Cov.: 34 AF XY: 0.603 AC XY: 44885 AN XY: 74382

African (AFR) AF: 0.574 AC: 23823 AN: 41478

American (AMR) AF: 0.698 AC: 10677 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.468 AC: 1624 AN: 3472

East Asian (EAS) AF: 0.505 AC: 2611 AN: 5170

South Asian (SAS) AF: 0.731 AC: 3524 AN: 4824

European-Finnish (FIN) AF: 0.600 AC: 6357 AN: 10588

Middle Eastern (MID) AF: 0.510 AC: 149 AN: 292

European-Non Finnish (NFE) AF: 0.597 AC: 40622 AN: 67998

Other (OTH) AF: 0.602 AC: 1271 AN: 2112

Alfa AF: 0.597 Hom.: 33693

Bravo AF: 0.602

Asia WGS AF: 0.622 AC: 2161 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	4.2
DANN	Benign	0.29
PhyloP100		0.57

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: rs1325586;

hg19: chr10-3323773;