1-166205335-G-A

Variant names:

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

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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC112268276	XR_002958633.2	n.178+39281G>A		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000229588	ENST00000653824.3	n.220+39281G>A		intron_variant	Intron 1 of 2
ENSG00000229588	ENST00000829274.1	n.178+39281G>A		intron_variant	Intron 1 of 1
ENSG00000229588	ENST00000829275.1	n.189+39281G>A		intron_variant	Intron 1 of 1
ENSG00000229588	ENST00000829276.1	n.140+39281G>A		intron_variant	Intron 1 of 2

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 v4.3

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

Other links and lift over

dbSNP: rs1451606; hg19: chr1-166174572;