1-188116702-T-C

Variant names:

• chr1-188116702-T-C
• rs10489764
• ENST00000648838.2:n.534+19484T>C

Variant summary

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

The ENST00000648838.2(ENSG00000285894):​n.534+19484T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.254 in 151,952 control chromosomes in the GnomAD database, including 5,345 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 0.25 (5345 hom., cov: 32)
• Consequence: ENSG00000285894 ENST00000648838.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.620

Genes affected

ENSG00000285894 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.302 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
ENSG00000285894	ENST00000648838.2	n.534+19484T>C		intron_variant	Intron 3 of 3

Frequencies

GnomAD3 genomes AF: 0.254 AC: 38595 AN: 151834 Hom.: 5336 Cov.: 32

Gnomad AFR AF: 0.156

Gnomad AMI AF: 0.309

Gnomad AMR AF: 0.277

Gnomad ASJ AF: 0.317

Gnomad EAS AF: 0.198

Gnomad SAS AF: 0.175

Gnomad FIN AF: 0.312

Gnomad MID AF: 0.264

Gnomad NFE AF: 0.306

Gnomad OTH AF: 0.251

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

GnomAD4 genome AF: 0.254 AC: 38632 AN: 151952 Hom.: 5345 Cov.: 32 AF XY: 0.255 AC XY: 18964 AN XY: 74274

Gnomad4 AFR AF: 0.157

Gnomad4 AMR AF: 0.277

Gnomad4 ASJ AF: 0.317

Gnomad4 EAS AF: 0.198

Gnomad4 SAS AF: 0.175

Gnomad4 FIN AF: 0.312

Gnomad4 NFE AF: 0.306

Gnomad4 OTH AF: 0.253

Alfa AF: 0.297 Hom.: 13671

Bravo AF: 0.252

Asia WGS AF: 0.195 AC: 676 AN: 3458

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.92
DANN	Benign	0.46

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10489764; hg19: chr1-188085833;