rs10509200

Variant names:

• chr10-63866801-T-C
• rs10509200
• ENST00000444770.1:n.495-123468T>C

Variant summary

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

The ENST00000444770.1(ENSG00000228566):​n.495-123468T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.158 in 152,226 control chromosomes in the GnomAD database, including 2,305 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 0.16 (2305 hom., cov: 32)
• Consequence: ENSG00000228566 ENST00000444770.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.09
• Publications: 7 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=-0.75).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.213 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC101928859	XR_007062169.1	n.280+1278A>G		intron_variant	Intron 2 of 3
LOC101928859	XR_246119.4	n.280+1278A>G		intron_variant	Intron 2 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000228566	ENST00000444770.1	n.495-123468T>C		intron_variant	Intron 2 of 2	3
ENSG00000299544	ENST00000764485.1	n.500+1278A>G		intron_variant	Intron 2 of 3

Frequencies

GnomAD3 genomes AF: 0.158 AC: 24105 AN: 152108 Hom.: 2311 Cov.: 32

Gnomad AFR AF: 0.0611

Gnomad AMI AF: 0.110

Gnomad AMR AF: 0.131

Gnomad ASJ AF: 0.104

Gnomad EAS AF: 0.155

Gnomad SAS AF: 0.202

Gnomad FIN AF: 0.216

Gnomad MID AF: 0.0854

Gnomad NFE AF: 0.216

Gnomad OTH AF: 0.143

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

GnomAD4 genome AF: 0.158 AC: 24094 AN: 152226 Hom.: 2305 Cov.: 32 AF XY: 0.158 AC XY: 11745 AN XY: 74424

African (AFR) AF: 0.0613 AC: 2547 AN: 41550

American (AMR) AF: 0.130 AC: 1993 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.104 AC: 362 AN: 3470

East Asian (EAS) AF: 0.156 AC: 806 AN: 5180

South Asian (SAS) AF: 0.200 AC: 962 AN: 4818

European-Finnish (FIN) AF: 0.216 AC: 2287 AN: 10588

Middle Eastern (MID) AF: 0.0850 AC: 25 AN: 294

European-Non Finnish (NFE) AF: 0.216 AC: 14715 AN: 68008

Other (OTH) AF: 0.140 AC: 297 AN: 2114

Alfa AF: 0.189 Hom.: 5113

Bravo AF: 0.148

Asia WGS AF: 0.166 AC: 578 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.75
CADD	Benign	16
DANN	Benign	0.86
PhyloP100		1.1

Splicing

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

Other links and lift over

dbSNP: rs10509200; hg19: chr10-65626561;