chr6-32006941-G-A

Variant names:

• chr6-32006941-G-A
• rs28691121
• ENST00000342991.10:n.1081+30G>A

Variant summary

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

The ENST00000342991.10(ENSG00000290788):​n.1081+30G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0663 in 1,501,740 control chromosomes in the GnomAD database, including 7,988 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 0.099 (1188 hom., cov: 29)
  • Exomes 𝑓: 0.063 (6800 hom.)
• Consequence: ENSG00000290788 ENST00000342991.10 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.62
• Publications: 2 publications found

Genes affected

ENSG00000290788 (HGNC:):

CYP21A1P (HGNC:2599): (cytochrome P450 family 21 subfamily A member 1, pseudogene)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.181 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000342991.10. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CYP21A1P	NR_040090.1		n.1081+30G>A		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000290788	ENST00000342991.10	TSL:3	n.1081+30G>A		intron	N/A
	CYP21A1P	ENST00000354927.4	TSL:6	n.643+30G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0989 AC: 14185 AN: 143426 Hom.: 1183 Cov.: 29

Gnomad AFR AF: 0.185

Gnomad AMI AF: 0.156

Gnomad AMR AF: 0.0649

Gnomad ASJ AF: 0.0272

Gnomad EAS AF: 0.0297

Gnomad SAS AF: 0.0564

Gnomad FIN AF: 0.138

Gnomad MID AF: 0.0855

Gnomad NFE AF: 0.0609

Gnomad OTH AF: 0.0930

GnomAD2 exomes AF: 0.0653 AC: 10527 AN: 161144 AF XY: 0.0637

Gnomad AFR exome AF: 0.199

Gnomad AMR exome AF: 0.0410

Gnomad ASJ exome AF: 0.0326

Gnomad EAS exome AF: 0.0226

Gnomad FIN exome AF: 0.127

Gnomad NFE exome AF: 0.0582

Gnomad OTH exome AF: 0.0619

GnomAD4 exome AF: 0.0628 AC: 85308 AN: 1358200 Hom.: 6800 Cov.: 35 AF XY: 0.0623 AC XY: 41814 AN XY: 670754

African (AFR) AF: 0.185 AC: 5722 AN: 30920

American (AMR) AF: 0.0475 AC: 1754 AN: 36928

Ashkenazi Jewish (ASJ) AF: 0.0341 AC: 856 AN: 25090

East Asian (EAS) AF: 0.0507 AC: 1847 AN: 36444

South Asian (SAS) AF: 0.0550 AC: 4271 AN: 77658

European-Finnish (FIN) AF: 0.127 AC: 6137 AN: 48410

Middle Eastern (MID) AF: 0.0702 AC: 389 AN: 5544

European-Non Finnish (NFE) AF: 0.0581 AC: 60418 AN: 1040616

Other (OTH) AF: 0.0692 AC: 3914 AN: 56590

GnomAD4 genome AF: 0.0991 AC: 14224 AN: 143540 Hom.: 1188 Cov.: 29 AF XY: 0.0999 AC XY: 6991 AN XY: 69960

African (AFR) AF: 0.185 AC: 7130 AN: 38568

American (AMR) AF: 0.0650 AC: 957 AN: 14734

Ashkenazi Jewish (ASJ) AF: 0.0272 AC: 93 AN: 3414

East Asian (EAS) AF: 0.0297 AC: 148 AN: 4978

South Asian (SAS) AF: 0.0574 AC: 254 AN: 4426

European-Finnish (FIN) AF: 0.138 AC: 1364 AN: 9868

Middle Eastern (MID) AF: 0.0816 AC: 23 AN: 282

European-Non Finnish (NFE) AF: 0.0610 AC: 3927 AN: 64426

Other (OTH) AF: 0.0980 AC: 196 AN: 2000

Alfa AF: 0.0697 Hom.: 165

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.44
DANN	Benign	0.59
PhyloP100		-1.6

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Other links and lift over

dbSNP: rs28691121; hg19: chr6-31974718; COSMIC: COSV61590007;