rs1205863

chr6-11943293-T-G

Variant summary

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

The XR_001743976.2(LOC107986570):n.363-8242T>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 0.304 in 152,156 control chromosomes in the GnomAD database, including 12,321 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 0.30 (12321 hom., cov: 32)
• Consequence: LOC107986570 XR_001743976.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0510

Genes affected

LOC107986570 (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 (AFR) allele frequency at 95% confidence interval = 0.719 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC107986570	XR_001743976.2	n.363-8242T>G		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.303 AC: 46088 AN: 152038 Hom.: 12267 Cov.: 32

Gnomad AFR AF: 0.725

Gnomad AMI AF: 0.0197

Gnomad AMR AF: 0.192

Gnomad ASJ AF: 0.152

Gnomad EAS AF: 0.0556

Gnomad SAS AF: 0.0918

Gnomad FIN AF: 0.142

Gnomad MID AF: 0.358

Gnomad NFE AF: 0.141

Gnomad OTH AF: 0.305

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

GnomAD4 genome AF: 0.304 AC: 46195 AN: 152156 Hom.: 12321 Cov.: 32 AF XY: 0.296 AC XY: 22006 AN XY: 74388

Gnomad4 AFR AF: 0.726

Gnomad4 AMR AF: 0.192

Gnomad4 ASJ AF: 0.152

Gnomad4 EAS AF: 0.0551

Gnomad4 SAS AF: 0.0915

Gnomad4 FIN AF: 0.142

Gnomad4 NFE AF: 0.141

Gnomad4 OTH AF: 0.303

Alfa AF: 0.258 Hom.: 1512

Bravo AF: 0.325

Asia WGS AF: 0.108 AC: 379 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	1.8
Dann	Benign	0.73

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1205863; hg19: chr6-11943526;