1-166259149-C-T

Variant names:

• chr1-166259149-C-T
• rs1432120
• ENST00000653824.3:n.221-76179C>T

Variant summary

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

The ENST00000653824.3(ENSG00000229588):​n.221-76179C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.879 in 151,902 control chromosomes in the GnomAD database, including 60,010 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 0.88 (60010 hom., cov: 31)
• Consequence: ENSG00000229588 ENST00000653824.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.921
• Publications: 1 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=-1.03).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.98 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.221-76179C>T		intron	N/A
	ENSG00000229588	ENST00000829274.1		n.179-79751C>T		intron	N/A
	ENSG00000229588	ENST00000829275.1		n.190-76179C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.879 AC: 133429 AN: 151784 Hom.: 59995 Cov.: 31

Gnomad AFR AF: 0.687

Gnomad AMI AF: 1.00

Gnomad AMR AF: 0.815

Gnomad ASJ AF: 0.993

Gnomad EAS AF: 0.845

Gnomad SAS AF: 0.964

Gnomad FIN AF: 0.956

Gnomad MID AF: 0.987

Gnomad NFE AF: 0.986

Gnomad OTH AF: 0.897

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

GnomAD4 genome AF: 0.879 AC: 133488 AN: 151902 Hom.: 60010 Cov.: 31 AF XY: 0.876 AC XY: 65053 AN XY: 74246

African (AFR) AF: 0.686 AC: 28401 AN: 41386

American (AMR) AF: 0.815 AC: 12441 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.993 AC: 3449 AN: 3472

East Asian (EAS) AF: 0.845 AC: 4377 AN: 5180

South Asian (SAS) AF: 0.965 AC: 4651 AN: 4822

European-Finnish (FIN) AF: 0.956 AC: 10068 AN: 10536

Middle Eastern (MID) AF: 0.986 AC: 290 AN: 294

European-Non Finnish (NFE) AF: 0.986 AC: 67003 AN: 67924

Other (OTH) AF: 0.899 AC: 1896 AN: 2108

Alfa AF: 0.951 Hom.: 243157

Bravo AF: 0.857

Asia WGS AF: 0.889 AC: 3057 AN: 3438

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	2.1
DANN	Benign	0.42
PhyloP100		-0.92

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: rs1432120;

hg19: chr1-166228386;