rs2040499

Variant names:

• chr7-92180343-C-G
• rs2040499
• ENST00000692281.1:c.2025+32852G>C

Variant summary

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

The ENST00000458493.6(ENSG00000285953):​c.2026-21140G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.446 in 152,060 control chromosomes in the GnomAD database, including 16,201 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 0.45 (16201 hom., cov: 32)
  • Exomes 𝑓: 0.28 (0 hom.)
• Consequence: ENSG00000285953 ENST00000458493.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.432
• Publications: 10 publications found

Genes affected

ENSG00000289027 (HGNC:):

CYP51A1-AS1 (HGNC:50694): (CYP51A1 antisense RNA 1)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.77).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.611 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000458493.6. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CYP51A1-AS1	NR_122109.1		n.2616C>G		non_coding_transcript_exon	Exon 5 of 5
	CYP51A1-AS1	NR_122110.1		n.2098C>G		non_coding_transcript_exon	Exon 3 of 3

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000289027	ENST00000692281.1		c.2025+32852G>C		intron	N/A	ENSP00000510568.1	A0A8I5KWQ7
	ENSG00000285953	ENST00000458493.6	TSL:4	c.2026-21140G>C		intron	N/A	ENSP00000396352.2	C9JD81
	ENSG00000285953	ENST00000650585.2		c.2026-21140G>C		intron	N/A	ENSP00000498010.2	A0A3B3ITR4

Frequencies

GnomAD3 genomes AF: 0.446 AC: 67788 AN: 151924 Hom.: 16173 Cov.: 32

Gnomad AFR AF: 0.617

Gnomad AMI AF: 0.235

Gnomad AMR AF: 0.378

Gnomad ASJ AF: 0.543

Gnomad EAS AF: 0.203

Gnomad SAS AF: 0.364

Gnomad FIN AF: 0.377

Gnomad MID AF: 0.392

Gnomad NFE AF: 0.391

Gnomad OTH AF: 0.452

GnomAD4 exome AF: 0.278 AC: 5 AN: 18 Hom.: 0 Cov.: 0 AF XY: 0.250 AC XY: 4 AN XY: 16

African (AFR) AC: 0 AN: 0

American (AMR) AF: 0.500 AC: 1 AN: 2

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AF: 0.00 AC: 0 AN: 2

European-Finnish (FIN) AF: 0.500 AC: 2 AN: 4

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.200 AC: 2 AN: 10

Other (OTH) AC: 0 AN: 0

GnomAD4 genome AF: 0.446 AC: 67870 AN: 152042 Hom.: 16201 Cov.: 32 AF XY: 0.442 AC XY: 32814 AN XY: 74298

African (AFR) AF: 0.617 AC: 25582 AN: 41468

American (AMR) AF: 0.378 AC: 5768 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.543 AC: 1883 AN: 3470

East Asian (EAS) AF: 0.203 AC: 1048 AN: 5172

South Asian (SAS) AF: 0.365 AC: 1760 AN: 4816

European-Finnish (FIN) AF: 0.377 AC: 3983 AN: 10578

Middle Eastern (MID) AF: 0.405 AC: 119 AN: 294

European-Non Finnish (NFE) AF: 0.391 AC: 26563 AN: 67968

Other (OTH) AF: 0.452 AC: 950 AN: 2104

Alfa AF: 0.417 Hom.: 1713

Bravo AF: 0.453

Asia WGS AF: 0.336 AC: 1172 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.77
CADD	Benign	12
DANN	Benign	0.80
PhyloP100		0.43

Splicing

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

Other links and lift over

dbSNP: rs2040499; hg19: chr7-91809657;