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

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000203825	ENST00000449715.1	n.513+79T>A		intron_variant	Intron 3 of 16	6

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 v4.3

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

Other links and lift over

dbSNP: rs11579261; hg19: chr1-149039120;