rs4769989

Positions:

• chr13-20300771-A-G

Variant summary

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

The XR_941720.2(LOC105370102):​n.106+4978A>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 0.545 in 152,006 control chromosomes in the GnomAD database, including 22,848 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 0.54 (22848 hom., cov: 32)
• Consequence: LOC105370102 XR_941720.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.455

Genes affected

LOC105370102 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.572 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC105370102	XR_941720.2	n.106+4978A>G		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.545 AC: 82741 AN: 151888 Hom.: 22824 Cov.: 32

Gnomad AFR AF: 0.545

Gnomad AMI AF: 0.626

Gnomad AMR AF: 0.531

Gnomad ASJ AF: 0.516

Gnomad EAS AF: 0.237

Gnomad SAS AF: 0.507

Gnomad FIN AF: 0.529

Gnomad MID AF: 0.481

Gnomad NFE AF: 0.577

Gnomad OTH AF: 0.536

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

GnomAD4 genome AF: 0.545 AC: 82812 AN: 152006 Hom.: 22848 Cov.: 32 AF XY: 0.539 AC XY: 40051 AN XY: 74300

Gnomad4 AFR AF: 0.545

Gnomad4 AMR AF: 0.531

Gnomad4 ASJ AF: 0.516

Gnomad4 EAS AF: 0.237

Gnomad4 SAS AF: 0.508

Gnomad4 FIN AF: 0.529

Gnomad4 NFE AF: 0.577

Gnomad4 OTH AF: 0.538

Alfa AF: 0.564 Hom.: 31681

Bravo AF: 0.545

Asia WGS AF: 0.445 AC: 1548 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	0.98
DANN	Benign	0.81

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4769989; hg19: chr13-20874910;