rs4939879

chr18-49619613-A-G

Variant summary

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

The XR_007066363.1(LOC105372112):n.178+6744A>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 0.485 in 151,934 control chromosomes in the GnomAD database, including 18,638 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 0.48 (18638 hom., cov: 32)
• Consequence: LOC105372112 XR_007066363.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0290

Genes affected

LOC105372112 (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 (AMR) allele frequency at 95% confidence interval = 0.544 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105372112	XR_007066363.1	n.178+6744A>G		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.485 AC: 73562 AN: 151816 Hom.: 18624 Cov.: 32

Gnomad AFR AF: 0.348

Gnomad AMI AF: 0.310

Gnomad AMR AF: 0.553

Gnomad ASJ AF: 0.524

Gnomad EAS AF: 0.412

Gnomad SAS AF: 0.504

Gnomad FIN AF: 0.583

Gnomad MID AF: 0.417

Gnomad NFE AF: 0.542

Gnomad OTH AF: 0.471

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

GnomAD4 genome AF: 0.485 AC: 73619 AN: 151934 Hom.: 18638 Cov.: 32 AF XY: 0.489 AC XY: 36305 AN XY: 74224

Gnomad4 AFR AF: 0.348

Gnomad4 AMR AF: 0.554

Gnomad4 ASJ AF: 0.524

Gnomad4 EAS AF: 0.412

Gnomad4 SAS AF: 0.507

Gnomad4 FIN AF: 0.583

Gnomad4 NFE AF: 0.542

Gnomad4 OTH AF: 0.469

Alfa AF: 0.529 Hom.: 22069

Bravo AF: 0.479

Asia WGS AF: 0.500 AC: 1737 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	8.3
Dann	Benign	0.75

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4939879; hg19: chr18-47145983;