rs7120739

Variant names:

• chr11-39142085-A-C
• rs7120739
• ENST00000649415.1:n.114+19440T>G

Your query was ambiguous. Multiple possible variants found:

• chr11-39142085-A-C
• chr11-39142085-A-G
• chr11-39142085-A-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000649415.1(ENSG00000285751):​n.114+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 ENST00000649415.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.77

Genes affected

ENSG00000285751 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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	ENST00000649415.1	n.114+19440T>G		intron_variant	Intron 1 of 2

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

Gnomad4 AFR AF: 0.672

Gnomad4 AMR AF: 0.853

Gnomad4 ASJ AF: 0.890

Gnomad4 EAS AF: 0.855

Gnomad4 SAS AF: 0.757

Gnomad4 FIN AF: 0.869

Gnomad4 NFE AF: 0.909

Gnomad4 OTH AF: 0.852

Alfa AF: 0.893 Hom.: 121585

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7120739; hg19: chr11-39163635;