NM_001394319.2:c.241-15C>T

Variant names:

• chr16-22166889-C-T
• rs8058588
• NM_001394319.2:c.241-15C>T

Variant summary

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

The NM_001394319.2(SDR42E2):​c.241-15C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0112 in 650,742 control chromosomes in the GnomAD database, including 355 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 0.032 (255 hom., cov: 32)
  • Exomes 𝑓: 0.0047 (100 hom.)
• Consequence: SDR42E2 NM_001394319.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.239
• Publications: 1 publications found

Genes affected

SDR42E2 (HGNC:35414): (short chain dehydrogenase/reductase family 42E, member 2) Predicted to enable oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor. Predicted to be involved in steroid biosynthetic process. [provided by Alliance of Genome Resources, Apr 2022]

ENSG00000301964 (HGNC:):

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 = 0.107 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001394319.2. 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
	SDR42E2	NM_001394319.2	MANE Select	c.241-15C>T		intron	N/A	NP_001381248.1
	SDR42E2	NM_001365288.2		c.853-15C>T		intron	N/A	NP_001352217.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SDR42E2	ENST00000602312.3	TSL:5 MANE Select	c.241-15C>T		intron	N/A	ENSP00000473474.2
	SDR42E2	ENST00000686682.1		c.853-15C>T		intron	N/A	ENSP00000509391.1
	SDR42E2	ENST00000684942.1		n.853-15C>T		intron	N/A	ENSP00000508835.1

Frequencies

GnomAD3 genomes AF: 0.0320 AC: 4873 AN: 152070 Hom.: 254 Cov.: 32

Gnomad AFR AF: 0.109

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0155

Gnomad ASJ AF: 0.000288

Gnomad EAS AF: 0.00424

Gnomad SAS AF: 0.00207

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00633

Gnomad NFE AF: 0.000368

Gnomad OTH AF: 0.0263

GnomAD2 exomes AF: 0.00729 AC: 867 AN: 118868 AF XY: 0.00552

Gnomad AFR exome AF: 0.108

Gnomad AMR exome AF: 0.00610

Gnomad ASJ exome AF: 0.000437

Gnomad EAS exome AF: 0.00280

Gnomad FIN exome AF: 0.00

Gnomad NFE exome AF: 0.000473

Gnomad OTH exome AF: 0.00518

GnomAD4 exome AF: 0.00474 AC: 2364 AN: 498554 Hom.: 100 Cov.: 0 AF XY: 0.00382 AC XY: 1018 AN XY: 266602

African (AFR) AF: 0.107 AC: 1584 AN: 14766

American (AMR) AF: 0.00632 AC: 201 AN: 31806

Ashkenazi Jewish (ASJ) AF: 0.000777 AC: 14 AN: 18020

East Asian (EAS) AF: 0.00174 AC: 54 AN: 31104

South Asian (SAS) AF: 0.00101 AC: 58 AN: 57476

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 32426

Middle Eastern (MID) AF: 0.0181 AC: 69 AN: 3820

European-Non Finnish (NFE) AF: 0.000345 AC: 97 AN: 281216

Other (OTH) AF: 0.0103 AC: 287 AN: 27920

GnomAD4 genome AF: 0.0322 AC: 4894 AN: 152188 Hom.: 255 Cov.: 32 AF XY: 0.0318 AC XY: 2363 AN XY: 74400

African (AFR) AF: 0.109 AC: 4539 AN: 41490

American (AMR) AF: 0.0155 AC: 237 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.000288 AC: 1 AN: 3468

East Asian (EAS) AF: 0.00425 AC: 22 AN: 5174

South Asian (SAS) AF: 0.00186 AC: 9 AN: 4826

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 10610

Middle Eastern (MID) AF: 0.00680 AC: 2 AN: 294

European-Non Finnish (NFE) AF: 0.000368 AC: 25 AN: 68016

Other (OTH) AF: 0.0280 AC: 59 AN: 2110

Alfa AF: 0.0119 Hom.: 82

Bravo AF: 0.0379

Asia WGS AF: 0.0290 AC: 102 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.52
DANN	Benign	0.62
PhyloP100		-0.24

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: rs8058588; hg19: chr16-22178210;