11-95689703-A-G

Variant names:

• chr11-95689703-A-G
• rs1939875
• ENST00000648353.1:n.526-55016A>G

Variant summary

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

The ENST00000648353.1(ENSG00000285842):​n.526-55016A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.742 in 152,004 control chromosomes in the GnomAD database, including 42,029 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 0.74 (42029 hom., cov: 31)
• Consequence: ENSG00000285842 ENST00000648353.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.546

Genes affected

ENSG00000285842 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.774 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
ENSG00000285842	ENST00000648353.1	n.526-55016A>G		intron_variant	Intron 3 of 4

Frequencies

GnomAD3 genomes AF: 0.742 AC: 112677 AN: 151886 Hom.: 41977 Cov.: 31

Gnomad AFR AF: 0.781

Gnomad AMI AF: 0.871

Gnomad AMR AF: 0.757

Gnomad ASJ AF: 0.741

Gnomad EAS AF: 0.743

Gnomad SAS AF: 0.709

Gnomad FIN AF: 0.719

Gnomad MID AF: 0.778

Gnomad NFE AF: 0.719

Gnomad OTH AF: 0.750

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

GnomAD4 genome AF: 0.742 AC: 112780 AN: 152004 Hom.: 42029 Cov.: 31 AF XY: 0.738 AC XY: 54855 AN XY: 74294

Gnomad4 AFR AF: 0.781

Gnomad4 AMR AF: 0.758

Gnomad4 ASJ AF: 0.741

Gnomad4 EAS AF: 0.743

Gnomad4 SAS AF: 0.709

Gnomad4 FIN AF: 0.719

Gnomad4 NFE AF: 0.719

Gnomad4 OTH AF: 0.743

Alfa AF: 0.722 Hom.: 82642

Bravo AF: 0.749

Asia WGS AF: 0.740 AC: 2574 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.34
DANN	Benign	0.53

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1939875; hg19: chr11-95422867;