rs10469900

Variant names:

• chr2-38139941-T-C
• rs10469900
• XR_001739413.2:n.2467A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The XR_001739413.2(LOC107985871):​n.2467A>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 0.274 in 152,028 control chromosomes in the GnomAD database, including 6,384 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 0.27 (6384 hom., cov: 32)
• Consequence: LOC107985871 XR_001739413.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.794
• Publications: 6 publications found

Genes affected

LOC107985871 (HGNC:):

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

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.406 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC107985871	XR_001739413.2	n.2467A>G		non_coding_transcript_exon_variant	Exon 3 of 3
LOC107985871	XR_007086290.1	n.3863A>G		non_coding_transcript_exon_variant	Exon 2 of 4
CYP1B1-AS1	NR_027252.1	n.190+8327T>C		intron_variant	Intron 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CYP1B1-AS1	ENST00000413828.3	n.214+8327T>C		intron_variant	Intron 3 of 3	5
ENSG00000227292	ENST00000450854.2	n.1192-17731A>G		intron_variant	Intron 6 of 6	4
CYP1B1-AS1	ENST00000585654.3	n.616+8327T>C		intron_variant	Intron 3 of 3	5

Frequencies

GnomAD3 genomes AF: 0.274 AC: 41552 AN: 151910 Hom.: 6360 Cov.: 32

Gnomad AFR AF: 0.411

Gnomad AMI AF: 0.416

Gnomad AMR AF: 0.222

Gnomad ASJ AF: 0.283

Gnomad EAS AF: 0.109

Gnomad SAS AF: 0.285

Gnomad FIN AF: 0.247

Gnomad MID AF: 0.285

Gnomad NFE AF: 0.216

Gnomad OTH AF: 0.242

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

GnomAD4 genome AF: 0.274 AC: 41624 AN: 152028 Hom.: 6384 Cov.: 32 AF XY: 0.275 AC XY: 20405 AN XY: 74320

African (AFR) AF: 0.411 AC: 17052 AN: 41440

American (AMR) AF: 0.221 AC: 3384 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.283 AC: 982 AN: 3470

East Asian (EAS) AF: 0.109 AC: 563 AN: 5170

South Asian (SAS) AF: 0.285 AC: 1375 AN: 4820

European-Finnish (FIN) AF: 0.247 AC: 2615 AN: 10572

Middle Eastern (MID) AF: 0.293 AC: 86 AN: 294

European-Non Finnish (NFE) AF: 0.216 AC: 14669 AN: 67964

Other (OTH) AF: 0.247 AC: 520 AN: 2108

Alfa AF: 0.254 Hom.: 1941

Bravo AF: 0.276

Asia WGS AF: 0.229 AC: 795 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	3.1
DANN	Benign	0.87
PhyloP100		-0.79

Splicing

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

Other links and lift over

dbSNP: rs10469900; hg19: chr2-38367083;