rs11129399

chr3-30354459-T-C

Variant summary

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

The XR_427323.4(LOC101927995):n.1149+3520T>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 0.115 in 152,094 control chromosomes in the GnomAD database, including 1,651 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 0.12 (1651 hom., cov: 32)
• Consequence: LOC101927995 XR_427323.4 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.396

Genes affected

LOC101927995 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.243 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC101927995	XR_427323.4	n.1149+3520T>C		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.115 AC: 17504 AN: 151974 Hom.: 1645 Cov.: 32

Gnomad AFR AF: 0.247

Gnomad AMI AF: 0.0757

Gnomad AMR AF: 0.0902

Gnomad ASJ AF: 0.104

Gnomad EAS AF: 0.209

Gnomad SAS AF: 0.167

Gnomad FIN AF: 0.0442

Gnomad MID AF: 0.127

Gnomad NFE AF: 0.0422

Gnomad OTH AF: 0.100

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

GnomAD4 genome AF: 0.115 AC: 17527 AN: 152094 Hom.: 1651 Cov.: 32 AF XY: 0.118 AC XY: 8755 AN XY: 74340

Gnomad4 AFR AF: 0.247

Gnomad4 AMR AF: 0.0901

Gnomad4 ASJ AF: 0.104

Gnomad4 EAS AF: 0.209

Gnomad4 SAS AF: 0.166

Gnomad4 FIN AF: 0.0442

Gnomad4 NFE AF: 0.0422

Gnomad4 OTH AF: 0.101

Alfa AF: 0.0602 Hom.: 879

Bravo AF: 0.125

Asia WGS AF: 0.175 AC: 608 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
Cadd	Benign	4.8
Dann	Benign	0.73

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11129399; hg19: chr3-30395951;