chr16-81997843-T-C

Variant names:

• chr16-81997843-T-C
• rs11443
• NM_145168.3:c.*1268A>G

Variant summary

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

The NM_145168.3(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 NM_145168.3 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.311
• Publications: 17 publications found

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

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_145168.3. 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
	SDR42E1	NM_145168.3	MANE Select	c.*1268A>G		3_prime_UTR	Exon 3 of 3	NP_660151.2

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SDR42E1	ENST00000328945.7	TSL:1 MANE Select	c.*1268A>G		3_prime_UTR	Exon 3 of 3	ENSP00000332407.4

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

⚠️ The allele balance in gnomAD version 4 Exomes is significantly skewed from the expected value of 0.5.

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AC: 0 AN: 0

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 2

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

Other (OTH) AC: 0 AN: 0

⚠️ The allele balance in gnomAD4 Exomes is highly skewed from 0.5 (p-value = 0.00233887), which strongly suggests a high chance of mosaicism in these individuals.

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

African (AFR) AF: 0.0724 AC: 3006 AN: 41542

American (AMR) AF: 0.285 AC: 4364 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.339 AC: 1178 AN: 3470

East Asian (EAS) AF: 0.102 AC: 530 AN: 5184

South Asian (SAS) AF: 0.326 AC: 1573 AN: 4822

European-Finnish (FIN) AF: 0.431 AC: 4561 AN: 10572

Middle Eastern (MID) AF: 0.284 AC: 83 AN: 292

European-Non Finnish (NFE) AF: 0.398 AC: 27063 AN: 67976

Other (OTH) AF: 0.301 AC: 634 AN: 2108

Alfa AF: 0.332 Hom.: 18490

Bravo AF: 0.262

Asia WGS AF: 0.230 AC: 803 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	3.0
DANN	Benign	0.76
PhyloP100		-0.31
Mutation Taster		=100/0	polymorphism (auto)

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: rs11443; hg19: chr16-82031448;