rs4568

chr14-24290803-G-A

Variant summary

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

The NM_001136050.3(DHRS1):c.*56C>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.292 in 1,604,948 control chromosomes in the GnomAD database, including 76,649 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 0.31 (7953 hom., cov: 29)
  • Exomes 𝑓: 0.29 (68696 hom.)
• Consequence: DHRS1 NM_001136050.3 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.415

Genes affected

DHRS1 (HGNC:16445): (dehydrogenase/reductase 1) This gene encodes a member of the short-chain dehydrogenases/reductases (SDR) family. The encoded enzyme contains a conserved catalytic domain and likely functions as an oxidoreductase. Multiple alternatively spliced variants, encoding the same protein, have been identified. [provided by RefSeq, Nov 2008]

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.689 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
DHRS1	NM_001136050.3	c.*56C>T		3_prime_UTR_variant	9/9	ENST00000288111.12

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
DHRS1	ENST00000288111.12	c.*56C>T		3_prime_UTR_variant	9/9	1	NM_001136050.3	P1
	ENST00000669726.3	n.111-7811G>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.311 AC: 46954 AN: 150944 Hom.: 7952 Cov.: 29

Gnomad AFR AF: 0.335

Gnomad AMI AF: 0.352

Gnomad AMR AF: 0.275

Gnomad ASJ AF: 0.300

Gnomad EAS AF: 0.708

Gnomad SAS AF: 0.519

Gnomad FIN AF: 0.355

Gnomad MID AF: 0.304

Gnomad NFE AF: 0.254

Gnomad OTH AF: 0.300

GnomAD4 exome AF: 0.290 AC: 421357 AN: 1453886 Hom.: 68696 Cov.: 31 AF XY: 0.296 AC XY: 214114 AN XY: 723098

Gnomad4 AFR exome AF: 0.332

Gnomad4 AMR exome AF: 0.286

Gnomad4 ASJ exome AF: 0.313

Gnomad4 EAS exome AF: 0.729

Gnomad4 SAS exome AF: 0.502

Gnomad4 FIN exome AF: 0.349

Gnomad4 NFE exome AF: 0.252

Gnomad4 OTH exome AF: 0.306

GnomAD4 genome AF: 0.311 AC: 46978 AN: 151062 Hom.: 7953 Cov.: 29 AF XY: 0.323 AC XY: 23842 AN XY: 73750

Gnomad4 AFR AF: 0.335

Gnomad4 AMR AF: 0.275

Gnomad4 ASJ AF: 0.300

Gnomad4 EAS AF: 0.709

Gnomad4 SAS AF: 0.518

Gnomad4 FIN AF: 0.355

Gnomad4 NFE AF: 0.254

Gnomad4 OTH AF: 0.306

Alfa AF: 0.274 Hom.: 12781

Bravo AF: 0.306

Asia WGS AF: 0.617 AC: 2144 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
Cadd	Benign	3.2
Dann	Benign	0.37

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: rs4568; hg19: chr14-24760009; COSMIC: COSV55384255; COSMIC: COSV55384255;