chr10-3281581-T-C

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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC107987146	XR_001747320.2	n.378-462T>C		intron_variant	Intron 1 of 1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000294649	ENST00000724949.1	n.109+4488T>C		intron_variant	Intron 1 of 3
ENSG00000294649	ENST00000724950.1	n.385+4488T>C		intron_variant	Intron 1 of 2
ENSG00000294649	ENST00000724951.1	n.35+4488T>C		intron_variant	Intron 1 of 1

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 v4.3

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

Other links and lift over

dbSNP: rs1325586; hg19: chr10-3323773;