rs1451606

Variant names:

• chr1-166205335-G-A
• rs1451606
• ENST00000653824.3:n.220+39281G>A

Your query was ambiguous. Multiple possible variants found:

• chr1-166205335-G-A
• chr1-166205335-G-T

Variant summary

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

The ENST00000653824.3(ENSG00000229588):​n.220+39281G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.67 in 152,048 control chromosomes in the GnomAD database, including 35,372 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 0.67 (35372 hom., cov: 33)
• Consequence: ENSG00000229588 ENST00000653824.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.610
• Publications: 3 publications found

Genes affected

ENSG00000229588 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.778 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000653824.3. 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
	ENSG00000229588	ENST00000653824.3		n.220+39281G>A		intron	N/A
	ENSG00000229588	ENST00000829274.1		n.178+39281G>A		intron	N/A
	ENSG00000229588	ENST00000829275.1		n.189+39281G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.670 AC: 101782 AN: 151930 Hom.: 35356 Cov.: 33

Gnomad AFR AF: 0.498

Gnomad AMI AF: 0.789

Gnomad AMR AF: 0.630

Gnomad ASJ AF: 0.692

Gnomad EAS AF: 0.490

Gnomad SAS AF: 0.618

Gnomad FIN AF: 0.769

Gnomad MID AF: 0.684

Gnomad NFE AF: 0.783

Gnomad OTH AF: 0.652

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

GnomAD4 genome AF: 0.670 AC: 101832 AN: 152048 Hom.: 35372 Cov.: 33 AF XY: 0.667 AC XY: 49521 AN XY: 74292

African (AFR) AF: 0.497 AC: 20620 AN: 41450

American (AMR) AF: 0.630 AC: 9613 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.692 AC: 2402 AN: 3470

East Asian (EAS) AF: 0.490 AC: 2534 AN: 5168

South Asian (SAS) AF: 0.619 AC: 2982 AN: 4814

European-Finnish (FIN) AF: 0.769 AC: 8127 AN: 10568

Middle Eastern (MID) AF: 0.684 AC: 201 AN: 294

European-Non Finnish (NFE) AF: 0.783 AC: 53255 AN: 67990

Other (OTH) AF: 0.651 AC: 1378 AN: 2116

Alfa AF: 0.704 Hom.: 6523

Bravo AF: 0.654

Asia WGS AF: 0.565 AC: 1967 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.85
DANN	Benign	0.75
PhyloP100		-0.61

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: rs1451606;

hg19: chr1-166174572;