rs1108101

Positions:

• chr22-20612170-G-A

Variant summary

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

The ENST00000416717.6(SMPD4P1):​n.862-1455C>T variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.306 in 152,222 control chromosomes in the GnomAD database, including 7,324 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 (7324 hom., cov: 34)
• Consequence: SMPD4P1 ENST00000416717.6 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.176

Genes affected

SMPD4P1 (HGNC:39673): (sphingomyelin phosphodiesterase 4 pseudogene 1)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.347 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SMPD4P1	ENST00000416717.6	n.862-1455C>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.306 AC: 46496 AN: 152104 Hom.: 7330 Cov.: 34

Gnomad AFR AF: 0.262

Gnomad AMI AF: 0.302

Gnomad AMR AF: 0.285

Gnomad ASJ AF: 0.247

Gnomad EAS AF: 0.144

Gnomad SAS AF: 0.224

Gnomad FIN AF: 0.348

Gnomad MID AF: 0.310

Gnomad NFE AF: 0.351

Gnomad OTH AF: 0.314

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

GnomAD4 genome AF: 0.306 AC: 46505 AN: 152222 Hom.: 7324 Cov.: 34 AF XY: 0.305 AC XY: 22689 AN XY: 74422

Gnomad4 AFR AF: 0.262

Gnomad4 AMR AF: 0.285

Gnomad4 ASJ AF: 0.247

Gnomad4 EAS AF: 0.144

Gnomad4 SAS AF: 0.226

Gnomad4 FIN AF: 0.348

Gnomad4 NFE AF: 0.351

Gnomad4 OTH AF: 0.311

Alfa AF: 0.336 Hom.: 11945

Bravo AF: 0.298

Asia WGS AF: 0.167 AC: 585 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.86
DANN	Benign	0.54

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1108101; hg19: chr22-20966457;