1-168494349-A-G

Variant names:

• chr1-168494349-A-G
• rs7417366
• ENST00000422253.1:n.58-225T>C

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The ENST00000422253.1(ENSG00000228697):​n.58-225T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.31 in 152,100 control chromosomes in the GnomAD database, including 8,612 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 0.31 (8612 hom., cov: 32)
• Consequence: ENSG00000228697 ENST00000422253.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.952
• Publications: 4 publications found

Genes affected

ENSG00000228697 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.28).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.566 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000422253.1. 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
	LOC101928565	NR_125956.2		n.54-225T>C		intron	N/A
	LOC101928565	NR_176056.1		n.54-162T>C		intron	N/A
	LOC101928565	NR_176057.1		n.54-206T>C		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000228697	ENST00000422253.1	TSL:1	n.58-225T>C		intron	N/A
	ENSG00000228697	ENST00000636459.1	TSL:5	n.99-206T>C		intron	N/A
	ENSG00000228697	ENST00000650143.1		n.56+1239T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.310 AC: 47078 AN: 151986 Hom.: 8610 Cov.: 32

Gnomad AFR AF: 0.119

Gnomad AMI AF: 0.436

Gnomad AMR AF: 0.398

Gnomad ASJ AF: 0.351

Gnomad EAS AF: 0.583

Gnomad SAS AF: 0.453

Gnomad FIN AF: 0.448

Gnomad MID AF: 0.294

Gnomad NFE AF: 0.350

Gnomad OTH AF: 0.314

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

GnomAD4 genome AF: 0.310 AC: 47082 AN: 152100 Hom.: 8612 Cov.: 32 AF XY: 0.320 AC XY: 23831 AN XY: 74366

African (AFR) AF: 0.118 AC: 4917 AN: 41526

American (AMR) AF: 0.398 AC: 6086 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.351 AC: 1214 AN: 3462

East Asian (EAS) AF: 0.584 AC: 3013 AN: 5162

South Asian (SAS) AF: 0.452 AC: 2182 AN: 4824

European-Finnish (FIN) AF: 0.448 AC: 4733 AN: 10558

Middle Eastern (MID) AF: 0.293 AC: 86 AN: 294

European-Non Finnish (NFE) AF: 0.350 AC: 23792 AN: 67970

Other (OTH) AF: 0.314 AC: 665 AN: 2116

Alfa AF: 0.346 Hom.: 13310

Bravo AF: 0.304

Asia WGS AF: 0.455 AC: 1576 AN: 3466

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.28
CADD	Benign	17
DANN	Benign	0.88
PhyloP100		0.95

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: rs7417366;

hg19: chr1-168463587;