rs28615950

Variant names:

• chr6-32006894-G-A
• rs28615950
• ENST00000342991.10:n.1064G>A

Your query was ambiguous. Multiple possible variants found:

• chr6-32006894-G-A
• chr6-32006894-G-C

Variant summary

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

The ENST00000342991.10(ENSG00000290788):​n.1064G>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 0.0947 in 1,506,258 control chromosomes in the GnomAD database, including 19,973 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 0.10 (1866 hom., cov: 29)
  • Exomes 𝑓: 0.094 (18107 hom.)
• Consequence: ENSG00000290788 ENST00000342991.10 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.696
• Publications: 5 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=-0.89).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.158 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CYP21A1P	NR_040090.1	n.1064G>A		non_coding_transcript_exon_variant	Exon 3 of 8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000290788	ENST00000342991.10	n.1064G>A		non_coding_transcript_exon_variant	Exon 3 of 8	3
CYP21A1P	ENST00000354927.4	n.626G>A		non_coding_transcript_exon_variant	Exon 5 of 10	6

Frequencies

GnomAD3 genomes AF: 0.105 AC: 15117 AN: 144392 Hom.: 1871 Cov.: 29

Gnomad AFR AF: 0.141

Gnomad AMI AF: 0.215

Gnomad AMR AF: 0.0778

Gnomad ASJ AF: 0.165

Gnomad EAS AF: 0.0372

Gnomad SAS AF: 0.169

Gnomad FIN AF: 0.0603

Gnomad MID AF: 0.105

Gnomad NFE AF: 0.0915

Gnomad OTH AF: 0.121

GnomAD2 exomes AF: 0.0995 AC: 16313 AN: 163982 AF XY: 0.103

Gnomad AFR exome AF: 0.153

Gnomad AMR exome AF: 0.0737

Gnomad ASJ exome AF: 0.173

Gnomad EAS exome AF: 0.0362

Gnomad FIN exome AF: 0.0608

Gnomad NFE exome AF: 0.0961

Gnomad OTH exome AF: 0.108

GnomAD4 exome AF: 0.0936 AC: 127503 AN: 1361756 Hom.: 18107 Cov.: 35 AF XY: 0.0950 AC XY: 63905 AN XY: 672492

African (AFR) AF: 0.156 AC: 4913 AN: 31446

American (AMR) AF: 0.0763 AC: 2868 AN: 37578

Ashkenazi Jewish (ASJ) AF: 0.171 AC: 4295 AN: 25104

East Asian (EAS) AF: 0.0204 AC: 753 AN: 36974

South Asian (SAS) AF: 0.151 AC: 11708 AN: 77792

European-Finnish (FIN) AF: 0.0603 AC: 2936 AN: 48680

Middle Eastern (MID) AF: 0.109 AC: 607 AN: 5576

European-Non Finnish (NFE) AF: 0.0897 AC: 93503 AN: 1041920

Other (OTH) AF: 0.104 AC: 5920 AN: 56686

GnomAD4 genome AF: 0.105 AC: 15117 AN: 144502 Hom.: 1866 Cov.: 29 AF XY: 0.104 AC XY: 7323 AN XY: 70466

African (AFR) AF: 0.141 AC: 5515 AN: 39154

American (AMR) AF: 0.0777 AC: 1144 AN: 14730

Ashkenazi Jewish (ASJ) AF: 0.165 AC: 562 AN: 3404

East Asian (EAS) AF: 0.0375 AC: 188 AN: 5012

South Asian (SAS) AF: 0.168 AC: 745 AN: 4438

European-Finnish (FIN) AF: 0.0603 AC: 600 AN: 9956

Middle Eastern (MID) AF: 0.0957 AC: 27 AN: 282

European-Non Finnish (NFE) AF: 0.0915 AC: 5919 AN: 64698

Other (OTH) AF: 0.119 AC: 238 AN: 1996

Alfa AF: 0.0705 Hom.: 169

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	3.3
DANN	Benign	0.80
PhyloP100		-0.70

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		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: rs28615950; hg19: chr6-31974671; COSMIC: COSV61590258;