6-159094277-T-G

Variant summary

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

The XM_047419645.1(LOC112267968):c.323+1452A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.76 in 152,342 control chromosomes in the GnomAD database, including 44,638 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 0.76 (44592 hom., cov: 33)
  • Exomes 𝑓: 0.76 (46 hom.)
• Consequence: LOC112267968 XM_047419645.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0310

Genes affected

LOC112267968 (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 (EAS) allele frequency at 95% confidence interval = 0.91 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC112267968	XM_047419645.1	c.323+1452A>C		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000642586.1	n.185T>G		non_coding_transcript_exon_variant	1/5
	ENST00000642829.1	n.500+1452A>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.760 AC: 115566 AN: 152076 Hom.: 44530 Cov.: 33

Gnomad AFR AF: 0.846

Gnomad AMI AF: 0.575

Gnomad AMR AF: 0.805

Gnomad ASJ AF: 0.671

Gnomad EAS AF: 0.932

Gnomad SAS AF: 0.792

Gnomad FIN AF: 0.788

Gnomad MID AF: 0.671

Gnomad NFE AF: 0.685

Gnomad OTH AF: 0.751

GnomAD4 exome AF: 0.757 AC: 112 AN: 148 Hom.: 46 Cov.: 0 AF XY: 0.755 AC XY: 83 AN XY: 110

Gnomad4 AFR exome AF: 1.00

Gnomad4 SAS exome AF: 0.900

Gnomad4 FIN exome AF: 0.800

Gnomad4 NFE exome AF: 0.733

Gnomad4 OTH exome AF: 0.875

GnomAD4 genome AF: 0.760 AC: 115687 AN: 152194 Hom.: 44592 Cov.: 33 AF XY: 0.768 AC XY: 57171 AN XY: 74412

Gnomad4 AFR AF: 0.846

Gnomad4 AMR AF: 0.805

Gnomad4 ASJ AF: 0.671

Gnomad4 EAS AF: 0.932

Gnomad4 SAS AF: 0.791

Gnomad4 FIN AF: 0.788

Gnomad4 NFE AF: 0.685

Gnomad4 OTH AF: 0.754

Alfa AF: 0.715 Hom.: 16903

Bravo AF: 0.764

Asia WGS AF: 0.883 AC: 3070 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
Cadd	Benign	4.2
Dann	Benign	0.52

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2249937; hg19: chr6-159515309;