11-61026179-C-G

Variant names:

• chr11-61026179-C-G
• rs4939490
• ENST00000794255.1:n.136-12639G>C

Variant summary

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

The ENST00000794255.1(ENSG00000303405):​n.136-12639G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.393 in 151,892 control chromosomes in the GnomAD database, including 12,070 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 0.39 (12070 hom., cov: 31)
• Consequence: ENSG00000303405 ENST00000794255.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.54
• Publications: 37 publications found

Genes affected

ENSG00000303405 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.456 is higher than 0.05.

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
ENSG00000303405	ENST00000794255.1	n.136-12639G>C		intron_variant	Intron 1 of 1
ENSG00000303405	ENST00000794256.1	n.229-12639G>C		intron_variant	Intron 2 of 2
ENSG00000303405	ENST00000794257.1	n.350-12639G>C		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.393 AC: 59593 AN: 151774 Hom.: 12049 Cov.: 31

Gnomad AFR AF: 0.462

Gnomad AMI AF: 0.426

Gnomad AMR AF: 0.306

Gnomad ASJ AF: 0.555

Gnomad EAS AF: 0.333

Gnomad SAS AF: 0.370

Gnomad FIN AF: 0.282

Gnomad MID AF: 0.513

Gnomad NFE AF: 0.383

Gnomad OTH AF: 0.428

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

GnomAD4 genome AF: 0.393 AC: 59644 AN: 151892 Hom.: 12070 Cov.: 31 AF XY: 0.387 AC XY: 28762 AN XY: 74236

African (AFR) AF: 0.462 AC: 19116 AN: 41402

American (AMR) AF: 0.305 AC: 4669 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.555 AC: 1922 AN: 3462

East Asian (EAS) AF: 0.333 AC: 1715 AN: 5156

South Asian (SAS) AF: 0.370 AC: 1784 AN: 4818

European-Finnish (FIN) AF: 0.282 AC: 2982 AN: 10562

Middle Eastern (MID) AF: 0.514 AC: 150 AN: 292

European-Non Finnish (NFE) AF: 0.383 AC: 26014 AN: 67896

Other (OTH) AF: 0.429 AC: 905 AN: 2112

Alfa AF: 0.399 Hom.: 6855

Bravo AF: 0.402

Asia WGS AF: 0.348 AC: 1208 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.47
DANN	Benign	0.43
PhyloP100		-1.5

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs4939490; hg19: chr11-60793651;