8-56381357-T-C

Position:

• chr8-56381357-T-C

Variant summary

Our verdict is Benign. Variant got -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

Genes affected

SDR16C6P (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SDR16C6P	NR_103832.1	n.399+585A>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SDR16C6P	ENST00000517787.1	n.408+585A>G		intron_variant		3
SDR16C6P	ENST00000524136.6	n.698+598A>G		intron_variant		6

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

Gnomad4 AFR AF: 0.512

Gnomad4 AMR AF: 0.450

Gnomad4 ASJ AF: 0.336

Gnomad4 EAS AF: 0.391

Gnomad4 SAS AF: 0.390

Gnomad4 FIN AF: 0.309

Gnomad4 NFE AF: 0.315

Gnomad4 OTH AF: 0.395

Alfa AF: 0.360 Hom.: 3176

Bravo AF: 0.404

Asia WGS AF: 0.373 AC: 1299 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1821814; hg19: chr8-57293916;