ENST00000425900.1:n.81+13408C>T

Variant names:

• chr20-7083102-C-T
• rs10485710
• ENST00000425900.1:n.81+13408C>T

Variant summary

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

The ENST00000425900.1(ENSG00000232271):​n.81+13408C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0719 in 151,860 control chromosomes in the GnomAD database, including 1,054 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 0.072 (1054 hom., cov: 32)
• Consequence: ENSG00000232271 ENST00000425900.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.406
• Publications: 1 publications found

Genes affected

ENSG00000232271 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.219 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000425900.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

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

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000232271	ENST00000425900.1	TSL:2	n.81+13408C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0718 AC: 10889 AN: 151742 Hom.: 1049 Cov.: 32

Gnomad AFR AF: 0.223

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0363

Gnomad ASJ AF: 0.0257

Gnomad EAS AF: 0.00193

Gnomad SAS AF: 0.00788

Gnomad FIN AF: 0.00274

Gnomad MID AF: 0.0380

Gnomad NFE AF: 0.0122

Gnomad OTH AF: 0.0644

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

GnomAD4 genome AF: 0.0719 AC: 10914 AN: 151860 Hom.: 1054 Cov.: 32 AF XY: 0.0699 AC XY: 5186 AN XY: 74228

African (AFR) AF: 0.223 AC: 9224 AN: 41398

American (AMR) AF: 0.0360 AC: 548 AN: 15212

Ashkenazi Jewish (ASJ) AF: 0.0257 AC: 89 AN: 3468

East Asian (EAS) AF: 0.00194 AC: 10 AN: 5166

South Asian (SAS) AF: 0.00789 AC: 38 AN: 4818

European-Finnish (FIN) AF: 0.00274 AC: 29 AN: 10596

Middle Eastern (MID) AF: 0.0408 AC: 12 AN: 294

European-Non Finnish (NFE) AF: 0.0122 AC: 830 AN: 67894

Other (OTH) AF: 0.0637 AC: 134 AN: 2104

Alfa AF: 0.0901 Hom.: 552

Bravo AF: 0.0833

Asia WGS AF: 0.0250 AC: 89 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.7
DANN	Benign	0.74
PhyloP100		-0.41
Mutation Taster		=100/0	polymorphism

Splicing

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

Other links and lift over

dbSNP: rs10485710; hg19: chr20-7063749;