6-36674483-C-T

Position:

• chr6-36674483-C-T

Variant summary

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

The NR_109836.1(PANDAR):​n.644G>A variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.156 in 1,519,996 control chromosomes in the GnomAD database, including 25,145 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 0.22 (4690 hom., cov: 32)
  • Exomes 𝑓: 0.15 (20455 hom.)
• Consequence: PANDAR NR_109836.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.386

Genes affected

LAP3P2 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.66).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.407 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
PANDAR	NR_109836.1	n.644G>A		non_coding_transcript_exon_variant	1/1
LAP3P2		n.36674483C>T		intragenic_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LAP3P2	ENST00000454686.1	n.667C>T		non_coding_transcript_exon_variant	1/1	6
PANDAR	ENST00000629595.1	n.644G>A		non_coding_transcript_exon_variant	1/1	6

Frequencies

GnomAD3 genomes AF: 0.222 AC: 33773 AN: 151954 Hom.: 4670 Cov.: 32

Gnomad AFR AF: 0.344

Gnomad AMI AF: 0.143

Gnomad AMR AF: 0.323

Gnomad ASJ AF: 0.0957

Gnomad EAS AF: 0.423

Gnomad SAS AF: 0.122

Gnomad FIN AF: 0.118

Gnomad MID AF: 0.155

Gnomad NFE AF: 0.142

Gnomad OTH AF: 0.220

GnomAD4 exome AF: 0.148 AC: 202665 AN: 1367924 Hom.: 20455 Cov.: 26 AF XY: 0.146 AC XY: 100193 AN XY: 685374

Gnomad4 AFR exome AF: 0.331

Gnomad4 AMR exome AF: 0.419

Gnomad4 ASJ exome AF: 0.0926

Gnomad4 EAS exome AF: 0.467

Gnomad4 SAS exome AF: 0.110

Gnomad4 FIN exome AF: 0.112

Gnomad4 NFE exome AF: 0.125

Gnomad4 OTH exome AF: 0.156

GnomAD4 genome AF: 0.223 AC: 33846 AN: 152072 Hom.: 4690 Cov.: 32 AF XY: 0.223 AC XY: 16612 AN XY: 74352

Gnomad4 AFR AF: 0.344

Gnomad4 AMR AF: 0.324

Gnomad4 ASJ AF: 0.0957

Gnomad4 EAS AF: 0.422

Gnomad4 SAS AF: 0.122

Gnomad4 FIN AF: 0.118

Gnomad4 NFE AF: 0.142

Gnomad4 OTH AF: 0.219

Alfa AF: 0.0630 Hom.: 76

Bravo AF: 0.251

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.66
CADD	Benign	0.012
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: rs4714003; hg19: chr6-36642260; COSMIC: COSV55187275;