10-63943084-T-C

Variant names:

• chr10-63943084-T-C
• rs2252578
• ENST00000444770.1:n.495-47185T>C

Variant summary

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

The ENST00000444770.1(ENSG00000228566):​n.495-47185T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.462 in 152,100 control chromosomes in the GnomAD database, including 17,835 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 0.46 (17835 hom., cov: 32)
• Consequence: ENSG00000228566 ENST00000444770.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.228
• Publications: 2 publications found

Genes affected

ENSG00000228566 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.595 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000444770.1. 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
	ENSG00000228566	ENST00000444770.1	TSL:3	n.495-47185T>C		intron	N/A
	ENSG00000228566	ENST00000654191.1		n.408-47185T>C		intron	N/A
	ENSG00000228566	ENST00000660795.1		n.157-47185T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.462 AC: 70233 AN: 151982 Hom.: 17824 Cov.: 32

Gnomad AFR AF: 0.254

Gnomad AMI AF: 0.498

Gnomad AMR AF: 0.605

Gnomad ASJ AF: 0.686

Gnomad EAS AF: 0.601

Gnomad SAS AF: 0.506

Gnomad FIN AF: 0.459

Gnomad MID AF: 0.624

Gnomad NFE AF: 0.529

Gnomad OTH AF: 0.527

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

GnomAD4 genome AF: 0.462 AC: 70275 AN: 152100 Hom.: 17835 Cov.: 32 AF XY: 0.463 AC XY: 34464 AN XY: 74384

African (AFR) AF: 0.254 AC: 10557 AN: 41502

American (AMR) AF: 0.605 AC: 9252 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.686 AC: 2379 AN: 3468

East Asian (EAS) AF: 0.602 AC: 3104 AN: 5158

South Asian (SAS) AF: 0.507 AC: 2444 AN: 4824

European-Finnish (FIN) AF: 0.459 AC: 4860 AN: 10596

Middle Eastern (MID) AF: 0.634 AC: 185 AN: 292

European-Non Finnish (NFE) AF: 0.529 AC: 35923 AN: 67960

Other (OTH) AF: 0.530 AC: 1118 AN: 2110

Alfa AF: 0.517 Hom.: 77950

Bravo AF: 0.464

Asia WGS AF: 0.537 AC: 1865 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	5.8
DANN	Benign	0.71
PhyloP100		0.23

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: rs2252578;

hg19: chr10-65702844;