chr2-38187399-T-C

Position:

• chr2-38187399-T-C

Variant summary

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

The XR_007086289.1(LOC102723739):​n.13407A>G 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 0.235 in 151,644 control chromosomes in the GnomAD database, including 4,372 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 0.23 (4372 hom., cov: 30)
• Consequence: LOC102723739 XR_007086289.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.211

Genes affected

LOC102723739 (HGNC:):

CYP1B1-AS1 (HGNC:28543): (CYP1B1 antisense RNA 1)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.273 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC102723739	XR_007086289.1	n.13407A>G		non_coding_transcript_exon_variant	3/4
LOC102723739	XR_427020.4	n.174-321A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CYP1B1-AS1	ENST00000629773.2	n.474-44161T>C		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.235 AC: 35578 AN: 151526 Hom.: 4368 Cov.: 30

Gnomad AFR AF: 0.183

Gnomad AMI AF: 0.291

Gnomad AMR AF: 0.239

Gnomad ASJ AF: 0.312

Gnomad EAS AF: 0.0551

Gnomad SAS AF: 0.247

Gnomad FIN AF: 0.210

Gnomad MID AF: 0.259

Gnomad NFE AF: 0.277

Gnomad OTH AF: 0.252

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

GnomAD4 genome AF: 0.235 AC: 35603 AN: 151644 Hom.: 4372 Cov.: 30 AF XY: 0.233 AC XY: 17244 AN XY: 74096

Gnomad4 AFR AF: 0.183

Gnomad4 AMR AF: 0.239

Gnomad4 ASJ AF: 0.312

Gnomad4 EAS AF: 0.0548

Gnomad4 SAS AF: 0.249

Gnomad4 FIN AF: 0.210

Gnomad4 NFE AF: 0.277

Gnomad4 OTH AF: 0.251

Alfa AF: 0.268 Hom.: 3824

Bravo AF: 0.233

Asia WGS AF: 0.178 AC: 618 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	6.5
DANN	Benign	0.74

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs183487; hg19: chr2-38414541;