chr1-82299369-T-C

Variant names:

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

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 5 publications found

Genes affected

ENSG00000233290 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.161 AC: 6678 AN: 41512

American (AMR) AF: 0.0921 AC: 1405 AN: 15252

Ashkenazi Jewish (ASJ) AF: 0.102 AC: 353 AN: 3468

East Asian (EAS) AF: 0.0502 AC: 259 AN: 5160

South Asian (SAS) AF: 0.0213 AC: 103 AN: 4828

European-Finnish (FIN) AF: 0.0594 AC: 630 AN: 10614

Middle Eastern (MID) AF: 0.0374 AC: 11 AN: 294

European-Non Finnish (NFE) AF: 0.0609 AC: 4139 AN: 68010

Other (OTH) AF: 0.0990 AC: 209 AN: 2112

Alfa AF: 0.0728 Hom.: 1385

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
PhyloP100		-0.078

Splicing

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

Other links and lift over

dbSNP: rs1770678; hg19: chr1-82765052;