chr10-63917874-C-T

Variant names:

• chr10-63917874-C-T
• rs2244205
• ENST00000444770.1:n.495-72395C>T

Variant summary

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

The ENST00000444770.1(ENSG00000228566):​n.495-72395C>T 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 151,932 control chromosomes in the GnomAD database, including 27,673 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 (27673 hom., cov: 31)
• Consequence: ENSG00000228566 ENST00000444770.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0840
• Publications: 3 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=-0.72).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.687 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC124902439	XR_007062159.1	n.386+30198C>T		intron_variant	Intron 1 of 2
LOC124902439	XR_007062160.1	n.386+30198C>T		intron_variant	Intron 1 of 5
LOC124902439	XR_007062161.1	n.388+44898C>T		intron_variant	Intron 1 of 5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000228566	ENST00000444770.1	n.495-72395C>T		intron_variant	Intron 2 of 2	3
ENSG00000228566	ENST00000654191.1	n.407+44898C>T		intron_variant	Intron 1 of 5
ENSG00000228566	ENST00000660795.1	n.156+30786C>T		intron_variant	Intron 1 of 6

Frequencies

GnomAD3 genomes AF: 0.600 AC: 91126 AN: 151814 Hom.: 27645 Cov.: 31

Gnomad AFR AF: 0.507

Gnomad AMI AF: 0.486

Gnomad AMR AF: 0.698

Gnomad ASJ AF: 0.713

Gnomad EAS AF: 0.644

Gnomad SAS AF: 0.571

Gnomad FIN AF: 0.639

Gnomad MID AF: 0.693

Gnomad NFE AF: 0.622

Gnomad OTH AF: 0.641

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

GnomAD4 genome AF: 0.600 AC: 91201 AN: 151932 Hom.: 27673 Cov.: 31 AF XY: 0.603 AC XY: 44773 AN XY: 74240

African (AFR) AF: 0.507 AC: 21009 AN: 41424

American (AMR) AF: 0.698 AC: 10662 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.713 AC: 2466 AN: 3460

East Asian (EAS) AF: 0.645 AC: 3339 AN: 5176

South Asian (SAS) AF: 0.572 AC: 2750 AN: 4808

European-Finnish (FIN) AF: 0.639 AC: 6733 AN: 10540

Middle Eastern (MID) AF: 0.690 AC: 203 AN: 294

European-Non Finnish (NFE) AF: 0.622 AC: 42237 AN: 67938

Other (OTH) AF: 0.643 AC: 1359 AN: 2114

Alfa AF: 0.628 Hom.: 51042

Bravo AF: 0.602

Asia WGS AF: 0.584 AC: 2029 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.72
CADD	Benign	1.8
DANN	Benign	0.80
PhyloP100		-0.084

Splicing

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

Other links and lift over

dbSNP: rs2244205; hg19: chr10-65677634;