rs11579642

Variant names:

• chr1-51002880-C-T
• rs11579642
• ENST00000762606.1:n.231+1311C>T

Variant summary

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

The ENST00000762606.1(ENSG00000299324):​n.231+1311C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.322 in 152,014 control chromosomes in the GnomAD database, including 8,156 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 0.32 (8156 hom., cov: 32)
• Consequence: ENSG00000299324 ENST00000762606.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.88
• Publications: 4 publications found

Genes affected

ENSG00000299324 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.06).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.352 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000762606.1. 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
	ENSG00000299324	ENST00000762606.1		n.231+1311C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.322 AC: 48909 AN: 151898 Hom.: 8135 Cov.: 32

Gnomad AFR AF: 0.357

Gnomad AMI AF: 0.360

Gnomad AMR AF: 0.297

Gnomad ASJ AF: 0.399

Gnomad EAS AF: 0.142

Gnomad SAS AF: 0.338

Gnomad FIN AF: 0.203

Gnomad MID AF: 0.494

Gnomad NFE AF: 0.331

Gnomad OTH AF: 0.365

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

GnomAD4 genome AF: 0.322 AC: 48964 AN: 152014 Hom.: 8156 Cov.: 32 AF XY: 0.317 AC XY: 23553 AN XY: 74300

African (AFR) AF: 0.357 AC: 14790 AN: 41428

American (AMR) AF: 0.297 AC: 4531 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.399 AC: 1385 AN: 3468

East Asian (EAS) AF: 0.143 AC: 739 AN: 5174

South Asian (SAS) AF: 0.339 AC: 1631 AN: 4818

European-Finnish (FIN) AF: 0.203 AC: 2147 AN: 10586

Middle Eastern (MID) AF: 0.486 AC: 143 AN: 294

European-Non Finnish (NFE) AF: 0.331 AC: 22498 AN: 67944

Other (OTH) AF: 0.366 AC: 773 AN: 2114

Alfa AF: 0.319 Hom.: 1870

Bravo AF: 0.328

Asia WGS AF: 0.248 AC: 861 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.094
DANN	Benign	0.33
PhyloP100		-2.9

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: rs11579642;

hg19: chr1-51468552;