rs2112347

chr5-75719417-T-G

Variant summary

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

The NR_149046.1(LOC441087):n.154-518T>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 0.425 in 151,876 control chromosomes in the GnomAD database, including 14,112 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 0.43 (14112 hom., cov: 31)
• Consequence: LOC441087 NR_149046.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.20

Genes affected

LOC441087 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.537 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC441087	NR_149046.1	n.154-518T>G		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.425 AC: 64516 AN: 151756 Hom.: 14100 Cov.: 31

Gnomad AFR AF: 0.511

Gnomad AMI AF: 0.446

Gnomad AMR AF: 0.396

Gnomad ASJ AF: 0.428

Gnomad EAS AF: 0.554

Gnomad SAS AF: 0.555

Gnomad FIN AF: 0.416

Gnomad MID AF: 0.304

Gnomad NFE AF: 0.363

Gnomad OTH AF: 0.389

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

GnomAD4 genome AF: 0.425 AC: 64567 AN: 151876 Hom.: 14112 Cov.: 31 AF XY: 0.432 AC XY: 32064 AN XY: 74232

Gnomad4 AFR AF: 0.511

Gnomad4 AMR AF: 0.397

Gnomad4 ASJ AF: 0.428

Gnomad4 EAS AF: 0.554

Gnomad4 SAS AF: 0.554

Gnomad4 FIN AF: 0.416

Gnomad4 NFE AF: 0.363

Gnomad4 OTH AF: 0.390

Alfa AF: 0.379 Hom.: 12738

Bravo AF: 0.422

Asia WGS AF: 0.563 AC: 1954 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
Cadd	Benign	0.25
Dann	Benign	0.57

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2112347; hg19: chr5-75015242;