rs11750584

chr5-41093757-C-G

Variant summary

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

The XR_001742650.2(LOC105374739):n.692+10724C>G 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 0.408 in 151,842 control chromosomes in the GnomAD database, including 12,848 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 0.41 (12848 hom., cov: 32)
• Consequence: LOC105374739 XR_001742650.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0260

Genes affected

LOC105374739 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.452 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105374739	XR_001742650.2	n.692+10724C>G		intron_variant, non_coding_transcript_variant
LOC105374739	XR_001742651.2	n.102+9427C>G		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.408 AC: 61915 AN: 151724 Hom.: 12834 Cov.: 32

Gnomad AFR AF: 0.457

Gnomad AMI AF: 0.400

Gnomad AMR AF: 0.321

Gnomad ASJ AF: 0.337

Gnomad EAS AF: 0.158

Gnomad SAS AF: 0.275

Gnomad FIN AF: 0.454

Gnomad MID AF: 0.358

Gnomad NFE AF: 0.423

Gnomad OTH AF: 0.413

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

GnomAD4 genome AF: 0.408 AC: 61963 AN: 151842 Hom.: 12848 Cov.: 32 AF XY: 0.405 AC XY: 30042 AN XY: 74184

Gnomad4 AFR AF: 0.457

Gnomad4 AMR AF: 0.320

Gnomad4 ASJ AF: 0.337

Gnomad4 EAS AF: 0.159

Gnomad4 SAS AF: 0.275

Gnomad4 FIN AF: 0.454

Gnomad4 NFE AF: 0.423

Gnomad4 OTH AF: 0.409

Alfa AF: 0.421 Hom.: 1682

Bravo AF: 0.395

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
Cadd	Benign	1.6
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: rs11750584; hg19: chr5-41093859;