10-58460686-T-C

Variant names:

• chr10-58460686-T-C
• rs12247559
• ENST00000720299.1:n.532+11850T>C

Variant summary

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

The ENST00000720299.1(ENSG00000293977):​n.532+11850T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0586 in 152,220 control chromosomes in the GnomAD database, including 505 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 0.059 (505 hom., cov: 32)
• Consequence: ENSG00000293977 ENST00000720299.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.22
• Publications: 1 publications found

Genes affected

ENSG00000293977 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.144 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105378316	XR_007062374.1	n.96-6499T>C		intron_variant	Intron 1 of 3
LOC105378316	XR_945981.3	n.361-6499T>C		intron_variant	Intron 2 of 5
LOC105378316	XR_945982.3	n.361-6499T>C		intron_variant	Intron 2 of 5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000293977	ENST00000720299.1	n.532+11850T>C		intron_variant	Intron 1 of 1
ENSG00000293977	ENST00000720300.1	n.97+5851T>C		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.0586 AC: 8906 AN: 152102 Hom.: 506 Cov.: 32

Gnomad AFR AF: 0.147

Gnomad AMI AF: 0.0482

Gnomad AMR AF: 0.0350

Gnomad ASJ AF: 0.0320

Gnomad EAS AF: 0.000577

Gnomad SAS AF: 0.00704

Gnomad FIN AF: 0.0176

Gnomad MID AF: 0.0316

Gnomad NFE AF: 0.0261

Gnomad OTH AF: 0.0550

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

GnomAD4 genome AF: 0.0586 AC: 8917 AN: 152220 Hom.: 505 Cov.: 32 AF XY: 0.0567 AC XY: 4222 AN XY: 74436

African (AFR) AF: 0.147 AC: 6102 AN: 41488

American (AMR) AF: 0.0349 AC: 534 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.0320 AC: 111 AN: 3468

East Asian (EAS) AF: 0.000578 AC: 3 AN: 5188

South Asian (SAS) AF: 0.00705 AC: 34 AN: 4824

European-Finnish (FIN) AF: 0.0176 AC: 187 AN: 10620

Middle Eastern (MID) AF: 0.0340 AC: 10 AN: 294

European-Non Finnish (NFE) AF: 0.0261 AC: 1777 AN: 68018

Other (OTH) AF: 0.0544 AC: 115 AN: 2114

Alfa AF: 0.0174 Hom.: 12

Bravo AF: 0.0646

Asia WGS AF: 0.0120 AC: 43 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.12
DANN	Benign	0.34
PhyloP100		-1.2

Splicing

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

Other links and lift over

dbSNP: rs12247559; hg19: chr10-60220446;