rs6472258

chr8-66184244-A-C

Variant summary

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

The XR_002956713.2(LOC112268029):n.89-1253T>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 0.101 in 148,764 control chromosomes in the GnomAD database, including 1,215 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 0.10 (1215 hom., cov: 32)
• Consequence: LOC112268029 XR_002956713.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.599

Genes affected

LOC112268029 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.328 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC112268029	XR_002956713.2	n.89-1253T>G		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.100 AC: 14938 AN: 148654 Hom.: 1209 Cov.: 32

Gnomad AFR AF: 0.0901

Gnomad AMI AF: 0.0143

Gnomad AMR AF: 0.241

Gnomad ASJ AF: 0.0490

Gnomad EAS AF: 0.342

Gnomad SAS AF: 0.153

Gnomad FIN AF: 0.0547

Gnomad MID AF: 0.0538

Gnomad NFE AF: 0.0642

Gnomad OTH AF: 0.0939

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

GnomAD4 genome AF: 0.101 AC: 14959 AN: 148764 Hom.: 1215 Cov.: 32 AF XY: 0.105 AC XY: 7632 AN XY: 72850

Gnomad4 AFR AF: 0.0900

Gnomad4 AMR AF: 0.241

Gnomad4 ASJ AF: 0.0490

Gnomad4 EAS AF: 0.342

Gnomad4 SAS AF: 0.152

Gnomad4 FIN AF: 0.0547

Gnomad4 NFE AF: 0.0642

Gnomad4 OTH AF: 0.103

Alfa AF: 0.0803 Hom.: 107

Bravo AF: 0.114

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
Cadd	Benign	2.0
Dann	Benign	0.70

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6472258; hg19: chr8-67096479;