rs11935505

Positions:

• chr4-144305270-G-A

Variant summary

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

The XR_939273.3(LOC105377462):​n.241-22084C>T 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 0.14 in 152,012 control chromosomes in the GnomAD database, including 2,489 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 0.14 (2489 hom., cov: 32)
• Consequence: LOC105377462 XR_939273.3 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.765

Genes affected

LOC105377462 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.56).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.324 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105377462	XR_939273.3	n.241-22084C>T		intron_variant, non_coding_transcript_variant
LOC105377462	XR_939272.3	n.315-22084C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000648340.1	n.215-22084C>T		intron_variant, non_coding_transcript_variant
GUSBP5	ENST00000651102.1	n.1926-11541G>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.140 AC: 21291 AN: 151894 Hom.: 2483 Cov.: 32

Gnomad AFR AF: 0.328

Gnomad AMI AF: 0.0625

Gnomad AMR AF: 0.135

Gnomad ASJ AF: 0.0778

Gnomad EAS AF: 0.147

Gnomad SAS AF: 0.0383

Gnomad FIN AF: 0.0447

Gnomad MID AF: 0.0823

Gnomad NFE AF: 0.0534

Gnomad OTH AF: 0.132

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

GnomAD4 genome AF: 0.140 AC: 21332 AN: 152012 Hom.: 2489 Cov.: 32 AF XY: 0.138 AC XY: 10270 AN XY: 74308

Gnomad4 AFR AF: 0.328

Gnomad4 AMR AF: 0.135

Gnomad4 ASJ AF: 0.0778

Gnomad4 EAS AF: 0.146

Gnomad4 SAS AF: 0.0387

Gnomad4 FIN AF: 0.0447

Gnomad4 NFE AF: 0.0534

Gnomad4 OTH AF: 0.130

Alfa AF: 0.0686 Hom.: 747

Bravo AF: 0.157

Asia WGS AF: 0.110 AC: 383 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.56
CADD	Benign	1.8
DANN	Benign	0.59

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11935505; hg19: chr4-145226422;