1-82299369-T-C

Variant names:

• chr1-82299369-T-C
• rs1770678
• ENST00000650063.1:n.888-83597A>G

Variant summary

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

The ENST00000650063.1(ENSG00000233290):​n.888-83597A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0911 in 152,162 control chromosomes in the GnomAD database, including 839 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 0.091 (839 hom., cov: 32)
• Consequence: ENSG00000233290 ENST00000650063.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0780

Genes affected

ENSG00000233290 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.158 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
ENSG00000233290	ENST00000650063.1	n.888-83597A>G		intron_variant	Intron 6 of 6
ENSG00000233290	ENST00000653483.1	n.720-83597A>G		intron_variant	Intron 4 of 4

Frequencies

GnomAD3 genomes AF: 0.0908 AC: 13803 AN: 152044 Hom.: 824 Cov.: 32

Gnomad AFR AF: 0.160

Gnomad AMI AF: 0.0779

Gnomad AMR AF: 0.0924

Gnomad ASJ AF: 0.102

Gnomad EAS AF: 0.0501

Gnomad SAS AF: 0.0215

Gnomad FIN AF: 0.0594

Gnomad MID AF: 0.0348

Gnomad NFE AF: 0.0609

Gnomad OTH AF: 0.0990

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

GnomAD4 genome AF: 0.0911 AC: 13858 AN: 152162 Hom.: 839 Cov.: 32 AF XY: 0.0890 AC XY: 6618 AN XY: 74378

Gnomad4 AFR AF: 0.161

Gnomad4 AMR AF: 0.0921

Gnomad4 ASJ AF: 0.102

Gnomad4 EAS AF: 0.0502

Gnomad4 SAS AF: 0.0213

Gnomad4 FIN AF: 0.0594

Gnomad4 NFE AF: 0.0609

Gnomad4 OTH AF: 0.0990

Alfa AF: 0.0708 Hom.: 474

Bravo AF: 0.0979

Asia WGS AF: 0.0600 AC: 207 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	0.94
DANN	Benign	0.47

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1770678; hg19: chr1-82765052;