1-143544453-T-C

Variant names:

• chr1-143544453-T-C
• rs11579261
• ENST00000449715.1:n.513+79T>C

Variant summary

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

The ENST00000449715.1(ENSG00000203825):​n.513+79T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.772 in 655,426 control chromosomes in the GnomAD database, including 204,779 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 0.78 (46259 hom., cov: 28)
  • Exomes 𝑓: 0.77 (158520 hom.)
• Consequence: ENSG00000203825 ENST00000449715.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.161
• Publications: 7 publications found

Genes affected

ENSG00000203825 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.824 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000449715.1. 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
	ENSG00000203825	ENST00000449715.1	TSL:6	n.513+79T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.775 AC: 113457 AN: 146344 Hom.: 46218 Cov.: 28

Gnomad AFR AF: 0.761

Gnomad AMI AF: 0.675

Gnomad AMR AF: 0.760

Gnomad ASJ AF: 0.779

Gnomad EAS AF: 0.845

Gnomad SAS AF: 0.643

Gnomad FIN AF: 0.827

Gnomad MID AF: 0.674

Gnomad NFE AF: 0.785

Gnomad OTH AF: 0.763

GnomAD4 exome AF: 0.770 AC: 392131 AN: 508964 Hom.: 158520 AF XY: 0.762 AC XY: 208853 AN XY: 274248

African (AFR) AF: 0.765 AC: 11316 AN: 14786

American (AMR) AF: 0.763 AC: 23273 AN: 30510

Ashkenazi Jewish (ASJ) AF: 0.781 AC: 11483 AN: 14700

East Asian (EAS) AF: 0.857 AC: 27650 AN: 32248

South Asian (SAS) AF: 0.627 AC: 32937 AN: 52520

European-Finnish (FIN) AF: 0.826 AC: 33452 AN: 40514

Middle Eastern (MID) AF: 0.698 AC: 1419 AN: 2034

European-Non Finnish (NFE) AF: 0.779 AC: 229495 AN: 294428

Other (OTH) AF: 0.775 AC: 21106 AN: 27224

GnomAD4 genome AF: 0.775 AC: 113550 AN: 146462 Hom.: 46259 Cov.: 28 AF XY: 0.773 AC XY: 55133 AN XY: 71364

African (AFR) AF: 0.761 AC: 30757 AN: 40438

American (AMR) AF: 0.760 AC: 11057 AN: 14544

Ashkenazi Jewish (ASJ) AF: 0.779 AC: 2647 AN: 3400

East Asian (EAS) AF: 0.845 AC: 4116 AN: 4870

South Asian (SAS) AF: 0.644 AC: 2822 AN: 4384

European-Finnish (FIN) AF: 0.827 AC: 8331 AN: 10068

Middle Eastern (MID) AF: 0.692 AC: 198 AN: 286

European-Non Finnish (NFE) AF: 0.785 AC: 51483 AN: 65560

Other (OTH) AF: 0.761 AC: 1533 AN: 2014

Alfa AF: 0.747 Hom.: 13098

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	7.5
PhyloP100		0.16

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: rs11579261;

hg19: chr1-149039120;