chr11-39142085-A-C

Variant names:

• chr11-39142085-A-C
• rs7120739
• ENST00000649415.2:n.341+19440T>G

Variant summary

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

The ENST00000649415.2(ENSG00000285751):​n.341+19440T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.828 in 152,088 control chromosomes in the GnomAD database, including 52,923 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 0.83 (52923 hom., cov: 32)
• Consequence: ENSG00000285751 ENST00000649415.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.77
• Publications: 2 publications found

Genes affected

ENSG00000285751 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.903 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
ENSG00000285751	ENST00000649415.2	n.341+19440T>G		intron_variant	Intron 1 of 2
ENSG00000285751	ENST00000722718.1	n.343+19440T>G		intron_variant	Intron 1 of 5
ENSG00000285751	ENST00000722719.1	n.215+8700T>G		intron_variant	Intron 2 of 3

Frequencies

GnomAD3 genomes AF: 0.828 AC: 125889 AN: 151970 Hom.: 52914 Cov.: 32

Gnomad AFR AF: 0.673

Gnomad AMI AF: 0.940

Gnomad AMR AF: 0.852

Gnomad ASJ AF: 0.890

Gnomad EAS AF: 0.854

Gnomad SAS AF: 0.756

Gnomad FIN AF: 0.869

Gnomad MID AF: 0.860

Gnomad NFE AF: 0.909

Gnomad OTH AF: 0.851

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

GnomAD4 genome AF: 0.828 AC: 125943 AN: 152088 Hom.: 52923 Cov.: 32 AF XY: 0.827 AC XY: 61509 AN XY: 74346

African (AFR) AF: 0.672 AC: 27895 AN: 41484

American (AMR) AF: 0.853 AC: 13023 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.890 AC: 3088 AN: 3470

East Asian (EAS) AF: 0.855 AC: 4412 AN: 5162

South Asian (SAS) AF: 0.757 AC: 3642 AN: 4810

European-Finnish (FIN) AF: 0.869 AC: 9198 AN: 10580

Middle Eastern (MID) AF: 0.853 AC: 249 AN: 292

European-Non Finnish (NFE) AF: 0.909 AC: 61789 AN: 68000

Other (OTH) AF: 0.852 AC: 1790 AN: 2102

Alfa AF: 0.885 Hom.: 247602

Bravo AF: 0.822

Asia WGS AF: 0.809 AC: 2816 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.011
DANN	Benign	0.43
PhyloP100		-1.8

Splicing

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

Other links and lift over

dbSNP: rs7120739; hg19: chr11-39163635;