rs11128271

chr3-72460120-T-C

Variant summary

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

The XR_940961.3(LOC105377160):n.403+995T>C variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.884 in 152,098 control chromosomes in the GnomAD database, including 59,847 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 0.88 (59847 hom., cov: 33)
• Consequence: LOC105377160 XR_940961.3 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.565

Genes affected

LOC105377160 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.68).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.939 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105377160	XR_940961.3	n.403+995T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.884 AC: 134396 AN: 151978 Hom.: 59814 Cov.: 33

Gnomad AFR AF: 0.788

Gnomad AMI AF: 0.957

Gnomad AMR AF: 0.888

Gnomad ASJ AF: 0.970

Gnomad EAS AF: 0.821

Gnomad SAS AF: 0.837

Gnomad FIN AF: 0.877

Gnomad MID AF: 0.959

Gnomad NFE AF: 0.945

Gnomad OTH AF: 0.900

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

GnomAD4 genome AF: 0.884 AC: 134483 AN: 152098 Hom.: 59847 Cov.: 33 AF XY: 0.881 AC XY: 65473 AN XY: 74322

Gnomad4 AFR AF: 0.788

Gnomad4 AMR AF: 0.888

Gnomad4 ASJ AF: 0.970

Gnomad4 EAS AF: 0.821

Gnomad4 SAS AF: 0.838

Gnomad4 FIN AF: 0.877

Gnomad4 NFE AF: 0.945

Gnomad4 OTH AF: 0.897

Alfa AF: 0.917 Hom.: 13306

Bravo AF: 0.881

Asia WGS AF: 0.803 AC: 2793 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.68
Cadd	Benign	5.9
Dann	Benign	0.89

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11128271; hg19: chr3-72509271;