rs10508569

Variant names:

• chr10-18886661-A-T
• rs10508569
• ENST00000723466.1:n.345-42397A>T

Variant summary

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

The ENST00000723466.1(ENSG00000234244):​n.345-42397A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.212 in 152,186 control chromosomes in the GnomAD database, including 4,005 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 0.21 (4005 hom., cov: 33)
• Consequence: ENSG00000234244 ENST00000723466.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.555
• Publications: 0 publications found

Genes affected

ENSG00000234244 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.79).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.334 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000234244	ENST00000723466.1	n.345-42397A>T		intron_variant	Intron 5 of 7
ENSG00000234244	ENST00000723467.1	n.306-42397A>T		intron_variant	Intron 4 of 6

Frequencies

GnomAD3 genomes AF: 0.212 AC: 32250 AN: 152068 Hom.: 4000 Cov.: 33

Gnomad AFR AF: 0.339

Gnomad AMI AF: 0.231

Gnomad AMR AF: 0.250

Gnomad ASJ AF: 0.121

Gnomad EAS AF: 0.234

Gnomad SAS AF: 0.143

Gnomad FIN AF: 0.0965

Gnomad MID AF: 0.123

Gnomad NFE AF: 0.153

Gnomad OTH AF: 0.211

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

GnomAD4 genome AF: 0.212 AC: 32275 AN: 152186 Hom.: 4005 Cov.: 33 AF XY: 0.208 AC XY: 15480 AN XY: 74420

African (AFR) AF: 0.338 AC: 14044 AN: 41490

American (AMR) AF: 0.250 AC: 3817 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.121 AC: 420 AN: 3470

East Asian (EAS) AF: 0.234 AC: 1211 AN: 5174

South Asian (SAS) AF: 0.141 AC: 683 AN: 4828

European-Finnish (FIN) AF: 0.0965 AC: 1024 AN: 10610

Middle Eastern (MID) AF: 0.116 AC: 34 AN: 294

European-Non Finnish (NFE) AF: 0.153 AC: 10390 AN: 68010

Other (OTH) AF: 0.209 AC: 442 AN: 2110

Alfa AF: 0.182 Hom.: 391

Bravo AF: 0.238

Asia WGS AF: 0.201 AC: 698 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	5.9
DANN	Benign	0.86
PhyloP100		0.56

Splicing

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

Other links and lift over

dbSNP: rs10508569; hg19: chr10-19175590;