1-82605158-T-C

Variant names:

• chr1-82605158-T-C
• rs6689622
• ENST00000650063.1:n.475-49597A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000650063.1(ENSG00000233290):​n.475-49597A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.531 in 151,756 control chromosomes in the GnomAD database, including 21,702 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 0.53 (21702 hom., cov: 31)
• Consequence: ENSG00000233290 ENST00000650063.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0640
• Publications: 1 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=-0.97).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.78 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000650063.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000233290	ENST00000650063.1		n.475-49597A>G		intron	N/A
	ENSG00000233290	ENST00000653483.1		n.307-49597A>G		intron	N/A
	ENSG00000233290	ENST00000663002.2		n.167-49597A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.531 AC: 80547 AN: 151640 Hom.: 21682 Cov.: 31

Gnomad AFR AF: 0.498

Gnomad AMI AF: 0.521

Gnomad AMR AF: 0.577

Gnomad ASJ AF: 0.544

Gnomad EAS AF: 0.801

Gnomad SAS AF: 0.621

Gnomad FIN AF: 0.527

Gnomad MID AF: 0.554

Gnomad NFE AF: 0.514

Gnomad OTH AF: 0.536

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

GnomAD4 genome AF: 0.531 AC: 80607 AN: 151756 Hom.: 21702 Cov.: 31 AF XY: 0.533 AC XY: 39491 AN XY: 74132

African (AFR) AF: 0.498 AC: 20632 AN: 41400

American (AMR) AF: 0.578 AC: 8793 AN: 15224

Ashkenazi Jewish (ASJ) AF: 0.544 AC: 1885 AN: 3468

East Asian (EAS) AF: 0.801 AC: 4108 AN: 5130

South Asian (SAS) AF: 0.621 AC: 2992 AN: 4816

European-Finnish (FIN) AF: 0.527 AC: 5552 AN: 10530

Middle Eastern (MID) AF: 0.551 AC: 161 AN: 292

European-Non Finnish (NFE) AF: 0.514 AC: 34891 AN: 67884

Other (OTH) AF: 0.532 AC: 1121 AN: 2106

Alfa AF: 0.445 Hom.: 1926

Bravo AF: 0.535

Asia WGS AF: 0.686 AC: 2386 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	3.3
DANN	Benign	0.28
PhyloP100		-0.064

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs6689622;

hg19: chr1-83070841;