rs1821814

Variant names:

• chr8-56381357-T-C
• rs1821814
• ENST00000517787.1:n.408+585A>G

Your query was ambiguous. Multiple possible variants found:

• chr8-56381357-T-C
• chr8-56381357-T-G

Variant summary

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

The ENST00000517787.1(SDR16C6P):​n.408+585A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.389 in 151,792 control chromosomes in the GnomAD database, including 12,096 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 0.39 (12096 hom., cov: 31)
• Consequence: SDR16C6P ENST00000517787.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.423
• Publications: 1 publications found

Genes affected

SDR16C6P (HGNC:):

SDR16C6P (HGNC:35413): (short chain dehydrogenase/reductase family 16C member 6, pseudogene)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.506 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000517787.1. 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
	SDR16C6P	NR_103832.1		n.399+585A>G		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SDR16C6P	ENST00000517787.1	TSL:3	n.408+585A>G		intron	N/A
	SDR16C6P	ENST00000524136.6	TSL:6	n.698+598A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.389 AC: 58963 AN: 151674 Hom.: 12081 Cov.: 31

Gnomad AFR AF: 0.512

Gnomad AMI AF: 0.385

Gnomad AMR AF: 0.450

Gnomad ASJ AF: 0.336

Gnomad EAS AF: 0.391

Gnomad SAS AF: 0.392

Gnomad FIN AF: 0.309

Gnomad MID AF: 0.386

Gnomad NFE AF: 0.315

Gnomad OTH AF: 0.394

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.389 AC: 59021 AN: 151792 Hom.: 12096 Cov.: 31 AF XY: 0.389 AC XY: 28895 AN XY: 74188

African (AFR) AF: 0.512 AC: 21183 AN: 41410

American (AMR) AF: 0.450 AC: 6854 AN: 15236

Ashkenazi Jewish (ASJ) AF: 0.336 AC: 1163 AN: 3464

East Asian (EAS) AF: 0.391 AC: 2012 AN: 5148

South Asian (SAS) AF: 0.390 AC: 1874 AN: 4802

European-Finnish (FIN) AF: 0.309 AC: 3269 AN: 10582

Middle Eastern (MID) AF: 0.384 AC: 113 AN: 294

European-Non Finnish (NFE) AF: 0.315 AC: 21369 AN: 67834

Other (OTH) AF: 0.395 AC: 833 AN: 2110

Alfa AF: 0.361 Hom.: 4022

Bravo AF: 0.404

Asia WGS AF: 0.373 AC: 1299 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	2.2
DANN	Benign	0.27
PhyloP100		-0.42

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs1821814; hg19: chr8-57293916;