11-72809485-C-G

Position:

• chr11-72809485-C-G

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_Strong BS2

The XR_001748490.3(LOC107984421):​n.2482G>C variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00905 in 152,212 control chromosomes in the GnomAD database, including 11 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 0.0090 (11 hom., cov: 31)
• Consequence: LOC107984421 XR_001748490.3 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.410

Genes affected

LOC107984421 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -8 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.7).
• BS2: High Homozygotes in GnomAd4 at 11 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC107984421	XR_001748490.3	n.2482G>C		non_coding_transcript_exon_variant	2/2
LOC107984421	XR_007062771.1	n.1435+3148G>C		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000285693	ENST00000624670.2	n.483+956G>C		intron_variant		6

Frequencies

GnomAD3 genomes AF: 0.00905 AC: 1377 AN: 152094 Hom.: 11 Cov.: 31

Gnomad AFR AF: 0.00217

Gnomad AMI AF: 0.0396

Gnomad AMR AF: 0.00707

Gnomad ASJ AF: 0.0109

Gnomad EAS AF: 0.000192

Gnomad SAS AF: 0.00145

Gnomad FIN AF: 0.0210

Gnomad MID AF: 0.00633

Gnomad NFE AF: 0.0127

Gnomad OTH AF: 0.00478

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

GnomAD4 genome AF: 0.00905 AC: 1377 AN: 152212 Hom.: 11 Cov.: 31 AF XY: 0.00912 AC XY: 679 AN XY: 74430

Gnomad4 AFR AF: 0.00217

Gnomad4 AMR AF: 0.00706

Gnomad4 ASJ AF: 0.0109

Gnomad4 EAS AF: 0.000193

Gnomad4 SAS AF: 0.00145

Gnomad4 FIN AF: 0.0210

Gnomad4 NFE AF: 0.0127

Gnomad4 OTH AF: 0.00473

Alfa AF: 0.000286 Hom.: 7952

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.70
CADD	Benign	4.5
DANN	Benign	0.85

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4944804; hg19: chr11-72520530;