rs11579261

Variant names:

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

Your query was ambiguous. Multiple possible variants found:

• chr1-143544453-T-A
• chr1-143544453-T-C
• chr1-143544453-T-G

Variant summary

Our verdict is Benign. The variant received -8 ACMG points: 0P and 8B. BP4_Strong BS2

The ENST00000449715.1(ENSG00000203825):​n.513+79T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000671 in 656,036 control chromosomes in the GnomAD database, including 3 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 0.00010 (1 hom., cov: 28)
  • Exomes 𝑓: 0.000057 (2 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 -8 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BS2: High Homozygotes in GnomAdExome4 at 2 gene

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>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.000102 AC: 15 AN: 146414 Hom.: 1 Cov.: 28

Gnomad AFR AF: 0.00

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.000229

Gnomad OTH AF: 0.00

GnomAD4 exome AF: 0.0000569 AC: 29 AN: 509622 Hom.: 2 AF XY: 0.0000510 AC XY: 14 AN XY: 274594

African (AFR) AF: 0.00 AC: 0 AN: 14800

American (AMR) AF: 0.00 AC: 0 AN: 30626

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 14712

East Asian (EAS) AF: 0.00 AC: 0 AN: 32278

South Asian (SAS) AF: 0.00 AC: 0 AN: 52572

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 40578

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 2034

European-Non Finnish (NFE) AF: 0.0000950 AC: 28 AN: 294780

Other (OTH) AF: 0.0000367 AC: 1 AN: 27242

GnomAD4 genome AF: 0.000102 AC: 15 AN: 146414 Hom.: 1 Cov.: 28 AF XY: 0.0000561 AC XY: 4 AN XY: 71266

African (AFR) AF: 0.00 AC: 0 AN: 40342

American (AMR) AF: 0.00 AC: 0 AN: 14538

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 3400

East Asian (EAS) AF: 0.00 AC: 0 AN: 4882

South Asian (SAS) AF: 0.00 AC: 0 AN: 4390

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 10072

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 304

European-Non Finnish (NFE) AF: 0.000229 AC: 15 AN: 65592

Other (OTH) AF: 0.00 AC: 0 AN: 1994

Alfa AF: 0.00 Hom.: 13098

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	7.1
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;