rs11583328

Positions:

• chr1-201033045-G-A

Variant summary

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

The XR_922410.3(LOC101929305):​n.1123+1680G>A 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 0.195 in 152,178 control chromosomes in the GnomAD database, including 3,619 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 0.20 (3619 hom., cov: 32)
• Consequence: LOC101929305 XR_922410.3 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.115

Genes affected

LOC101929305 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.281 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC101929305	XR_922410.3	n.1123+1680G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000610411.1	n.96+1814G>A		intron_variant, non_coding_transcript_variant		4

Frequencies

GnomAD3 genomes AF: 0.195 AC: 29676 AN: 152060 Hom.: 3618 Cov.: 32

Gnomad AFR AF: 0.0887

Gnomad AMI AF: 0.439

Gnomad AMR AF: 0.153

Gnomad ASJ AF: 0.225

Gnomad EAS AF: 0.00558

Gnomad SAS AF: 0.101

Gnomad FIN AF: 0.204

Gnomad MID AF: 0.253

Gnomad NFE AF: 0.284

Gnomad OTH AF: 0.198

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

GnomAD4 genome AF: 0.195 AC: 29676 AN: 152178 Hom.: 3619 Cov.: 32 AF XY: 0.189 AC XY: 14038 AN XY: 74408

Gnomad4 AFR AF: 0.0887

Gnomad4 AMR AF: 0.152

Gnomad4 ASJ AF: 0.225

Gnomad4 EAS AF: 0.00559

Gnomad4 SAS AF: 0.102

Gnomad4 FIN AF: 0.204

Gnomad4 NFE AF: 0.284

Gnomad4 OTH AF: 0.196

Alfa AF: 0.225 Hom.: 1172

Bravo AF: 0.187

Asia WGS AF: 0.0630 AC: 221 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	2.0
DANN	Benign	0.78

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11583328; hg19: chr1-201002173;