ENST00000648995.1:n.211+32585C>T

Variant names:

• chr10-6770213-C-T
• rs1822279
• ENST00000648995.1:n.211+32585C>T

Variant summary

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

The ENST00000648995.1(ENSG00000285988):​n.211+32585C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.064 in 152,244 control chromosomes in the GnomAD database, including 906 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 0.064 (906 hom., cov: 32)
• Consequence: ENSG00000285988 ENST00000648995.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.116

Genes affected

ENSG00000285988 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.199 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
ENSG00000285988	ENST00000648995.1	n.211+32585C>T		intron_variant	Intron 1 of 3
ENSG00000285743	ENST00000650342.1	n.375-11091C>T		intron_variant	Intron 3 of 6

Frequencies

GnomAD3 genomes AF: 0.0639 AC: 9725 AN: 152126 Hom.: 902 Cov.: 32

Gnomad AFR AF: 0.203

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0275

Gnomad ASJ AF: 0.0268

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.0168

Gnomad FIN AF: 0.00245

Gnomad MID AF: 0.0823

Gnomad NFE AF: 0.00842

Gnomad OTH AF: 0.0521

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

GnomAD4 genome AF: 0.0640 AC: 9745 AN: 152244 Hom.: 906 Cov.: 32 AF XY: 0.0630 AC XY: 4693 AN XY: 74448

Gnomad4 AFR AF: 0.203

Gnomad4 AMR AF: 0.0274

Gnomad4 ASJ AF: 0.0268

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.0172

Gnomad4 FIN AF: 0.00245

Gnomad4 NFE AF: 0.00842

Gnomad4 OTH AF: 0.0516

Alfa AF: 0.0406 Hom.: 58

Bravo AF: 0.0717

Asia WGS AF: 0.0160 AC: 59 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	3.5
DANN	Benign	0.76

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1822279; hg19: chr10-6812175;