rs1108101

Variant names:

• chr22-20612170-G-A
• rs1108101

Variant summary

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

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 intragenic
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.176
• Publications: 1 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000416717.6. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SMPD4P1	ENST00000416717.6	TSL:6	n.862-1455C>T		intron	N/A

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

African (AFR) AF: 0.262 AC: 10867 AN: 41546

American (AMR) AF: 0.285 AC: 4357 AN: 15304

Ashkenazi Jewish (ASJ) AF: 0.247 AC: 859 AN: 3472

East Asian (EAS) AF: 0.144 AC: 744 AN: 5180

South Asian (SAS) AF: 0.226 AC: 1091 AN: 4828

European-Finnish (FIN) AF: 0.348 AC: 3685 AN: 10586

Middle Eastern (MID) AF: 0.313 AC: 92 AN: 294

European-Non Finnish (NFE) AF: 0.351 AC: 23879 AN: 67990

Other (OTH) AF: 0.311 AC: 656 AN: 2110

Alfa AF: 0.330 Hom.: 16033

Bravo AF: 0.298

Asia WGS AF: 0.167 AC: 585 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.86
DANN	Benign	0.54
PhyloP100		-0.18

Splicing

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

Other links and lift over

dbSNP: rs1108101; hg19: chr22-20966457;