rs1606303

chr8-23667231-C-G

Variant summary

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

The XR_001745842.2(LOC107986930):n.1205-1412C>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 0.511 in 151,920 control chromosomes in the GnomAD database, including 20,582 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 0.51 (20582 hom., cov: 33)
• Consequence: LOC107986930 XR_001745842.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0350

Genes affected

LOC107986930 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.675 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC107986930	XR_001745842.2	n.1205-1412C>G		intron_variant, non_coding_transcript_variant
LOC107986930	XR_001745841.2	n.583-1412C>G		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.511 AC: 77627 AN: 151802 Hom.: 20576 Cov.: 33

Gnomad AFR AF: 0.377

Gnomad AMI AF: 0.550

Gnomad AMR AF: 0.538

Gnomad ASJ AF: 0.578

Gnomad EAS AF: 0.694

Gnomad SAS AF: 0.560

Gnomad FIN AF: 0.494

Gnomad MID AF: 0.490

Gnomad NFE AF: 0.568

Gnomad OTH AF: 0.515

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

GnomAD4 genome AF: 0.511 AC: 77672 AN: 151920 Hom.: 20582 Cov.: 33 AF XY: 0.511 AC XY: 37934 AN XY: 74240

Gnomad4 AFR AF: 0.377

Gnomad4 AMR AF: 0.538

Gnomad4 ASJ AF: 0.578

Gnomad4 EAS AF: 0.694

Gnomad4 SAS AF: 0.561

Gnomad4 FIN AF: 0.494

Gnomad4 NFE AF: 0.569

Gnomad4 OTH AF: 0.513

Alfa AF: 0.533 Hom.: 2748

Bravo AF: 0.510

Asia WGS AF: 0.561 AC: 1949 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
Cadd	Benign	2.3
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: rs1606303; hg19: chr8-23524744;