ENST00000649548.1:n.199+236T>C

Variant names:

• chr10-62685804-A-G
• rs10761659
• ENST00000649548.1:n.199+236T>C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000649548.1(ENSG00000238280):​n.199+236T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.438 in 152,152 control chromosomes in the GnomAD database, including 17,602 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 0.44 (17602 hom., cov: 32)
• Consequence: ENSG00000238280 ENST00000649548.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.596

Genes affected

ENSG00000238280 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.742 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
ENSG00000238280	ENST00000649548.1	n.199+236T>C		intron_variant	Intron 2 of 3

Frequencies

GnomAD3 genomes AF: 0.438 AC: 66642 AN: 152034 Hom.: 17594 Cov.: 32

Gnomad AFR AF: 0.136

Gnomad AMI AF: 0.542

Gnomad AMR AF: 0.542

Gnomad ASJ AF: 0.543

Gnomad EAS AF: 0.761

Gnomad SAS AF: 0.641

Gnomad FIN AF: 0.516

Gnomad MID AF: 0.449

Gnomad NFE AF: 0.541

Gnomad OTH AF: 0.443

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

GnomAD4 genome AF: 0.438 AC: 66646 AN: 152152 Hom.: 17602 Cov.: 32 AF XY: 0.444 AC XY: 33053 AN XY: 74394

Gnomad4 AFR AF: 0.136

Gnomad4 AMR AF: 0.543

Gnomad4 ASJ AF: 0.543

Gnomad4 EAS AF: 0.762

Gnomad4 SAS AF: 0.640

Gnomad4 FIN AF: 0.516

Gnomad4 NFE AF: 0.541

Gnomad4 OTH AF: 0.439

Alfa AF: 0.526 Hom.: 34135

Bravo AF: 0.424

Asia WGS AF: 0.607 AC: 2109 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	1.7
DANN	Benign	0.78

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10761659; hg19: chr10-64445564;