16-81997843-T-C

Position:

• chr16-81997843-T-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000328945.7(SDR42E1):​c.*1268A>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.285 in 152,180 control chromosomes in the GnomAD database, including 7,823 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 0.28 (7823 hom., cov: 32)
  • Exomes 𝑓: 0.33 (0 hom.)
• Consequence: SDR42E1 ENST00000328945.7 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.311

Genes affected

SDR42E1 (HGNC:29834): (short chain dehydrogenase/reductase family 42E, member 1) 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. Predicted to be integral component of membrane. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.394 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SDR42E1	NM_145168.3	c.*1268A>G		3_prime_UTR_variant	3/3	ENST00000328945.7	NP_660151.2
SDR42E1	XM_005256257.5	c.*1268A>G		3_prime_UTR_variant	4/4		XP_005256314.1
SDR42E1	XM_011523471.4	c.*1268A>G		3_prime_UTR_variant	3/3		XP_011521773.1
SDR42E1	XM_047434925.1	c.*1268A>G		3_prime_UTR_variant	3/3		XP_047290881.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SDR42E1	ENST00000328945.7	c.*1268A>G		3_prime_UTR_variant	3/3	1	NM_145168.3	ENSP00000332407	P1

Frequencies

GnomAD3 genomes AF: 0.285 AC: 43314 AN: 152056 Hom.: 7816 Cov.: 32

Gnomad AFR AF: 0.0725

Gnomad AMI AF: 0.360

Gnomad AMR AF: 0.286

Gnomad ASJ AF: 0.339

Gnomad EAS AF: 0.103

Gnomad SAS AF: 0.325

Gnomad FIN AF: 0.431

Gnomad MID AF: 0.283

Gnomad NFE AF: 0.398

Gnomad OTH AF: 0.301

GnomAD4 exome AF: 0.333 AC: 2 AN: 6 Hom.: 0 Cov.: 0 AF XY: 0.333 AC XY: 2 AN XY: 6

Gnomad4 NFE exome AF: 0.500

GnomAD4 genome AF: 0.285 AC: 43320 AN: 152174 Hom.: 7823 Cov.: 32 AF XY: 0.289 AC XY: 21477 AN XY: 74398

Gnomad4 AFR AF: 0.0724

Gnomad4 AMR AF: 0.285

Gnomad4 ASJ AF: 0.339

Gnomad4 EAS AF: 0.102

Gnomad4 SAS AF: 0.326

Gnomad4 FIN AF: 0.431

Gnomad4 NFE AF: 0.398

Gnomad4 OTH AF: 0.301

Alfa AF: 0.359 Hom.: 14196

Bravo AF: 0.262

Asia WGS AF: 0.230 AC: 803 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	3.0
DANN	Benign	0.76

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

Publications

LitVar

Other links and lift over

dbSNP: rs11443; hg19: chr16-82031448;