rs16845869

chr3-130758722-T-G

Variant summary

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

The XR_001740492.2(LOC107986023):n.1219-7325A>C 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 0.0764 in 152,250 control chromosomes in the GnomAD database, including 729 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 0.076 (729 hom., cov: 32)
• Consequence: LOC107986023 XR_001740492.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.03

Genes affected

LOC107986023 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.208 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC107986023	XR_001740492.2	n.1219-7325A>C		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.0763 AC: 11613 AN: 152132 Hom.: 720 Cov.: 32

Gnomad AFR AF: 0.0291

Gnomad AMI AF: 0.00987

Gnomad AMR AF: 0.214

Gnomad ASJ AF: 0.0941

Gnomad EAS AF: 0.117

Gnomad SAS AF: 0.107

Gnomad FIN AF: 0.0878

Gnomad MID AF: 0.108

Gnomad NFE AF: 0.0667

Gnomad OTH AF: 0.0883

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

GnomAD4 genome AF: 0.0764 AC: 11638 AN: 152250 Hom.: 729 Cov.: 32 AF XY: 0.0825 AC XY: 6145 AN XY: 74442

Gnomad4 AFR AF: 0.0291

Gnomad4 AMR AF: 0.214

Gnomad4 ASJ AF: 0.0941

Gnomad4 EAS AF: 0.117

Gnomad4 SAS AF: 0.108

Gnomad4 FIN AF: 0.0878

Gnomad4 NFE AF: 0.0667

Gnomad4 OTH AF: 0.0917

Alfa AF: 0.0747 Hom.: 742

Bravo AF: 0.0854

Asia WGS AF: 0.115 AC: 401 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
Cadd	Benign	11
Dann	Benign	0.38

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs16845869; hg19: chr3-130477566;