2-131501020-A-G

Variant names:

• chr2-131501020-A-G
• rs13415770
• ENST00000438378.3:n.777A>G

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The ENST00000438378.3(SMPD4BP):​n.777A>G variant causes a non coding transcript exon change. The variant allele was found at a frequency of 0.211 in 1,612,642 control chromosomes in the GnomAD database, including 46,121 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 0.19 (4396 hom., cov: 33)
  • Exomes 𝑓: 0.21 (41725 hom.)
• Consequence: SMPD4BP ENST00000438378.3 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 6.65
• Publications: 5 publications found

Genes affected

SMPD4BP (HGNC:):

SMPD4BP (HGNC:24761): (sphingomyelin phosphodiesterase 4B, pseudogene)

ACMG classification

Our verdict: Benign. The variant received -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.34).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.651 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000438378.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SMPD4BP	NR_026922.1		n.777A>G		non_coding_transcript_exon	Exon 6 of 18

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SMPD4BP	ENST00000438378.3	TSL:1	n.777A>G		non_coding_transcript_exon	Exon 6 of 18
	SMPD4BP	ENST00000415574.6	TSL:6	n.777A>G		non_coding_transcript_exon	Exon 6 of 19
	SMPD4BP	ENST00000685161.1		n.966A>G		non_coding_transcript_exon	Exon 3 of 3

Frequencies

GnomAD3 genomes AF: 0.194 AC: 29512 AN: 151978 Hom.: 4386 Cov.: 33

Gnomad AFR AF: 0.0459

Gnomad AMI AF: 0.257

Gnomad AMR AF: 0.382

Gnomad ASJ AF: 0.305

Gnomad EAS AF: 0.671

Gnomad SAS AF: 0.294

Gnomad FIN AF: 0.272

Gnomad MID AF: 0.225

Gnomad NFE AF: 0.179

Gnomad OTH AF: 0.236

GnomAD4 exome AF: 0.213 AC: 310923 AN: 1460550 Hom.: 41725 Cov.: 35 AF XY: 0.214 AC XY: 155625 AN XY: 726510

African (AFR) AF: 0.0380 AC: 1272 AN: 33438

American (AMR) AF: 0.489 AC: 21758 AN: 44506

Ashkenazi Jewish (ASJ) AF: 0.310 AC: 8104 AN: 26110

East Asian (EAS) AF: 0.694 AC: 27506 AN: 39628

South Asian (SAS) AF: 0.281 AC: 24195 AN: 86140

European-Finnish (FIN) AF: 0.265 AC: 14112 AN: 53328

Middle Eastern (MID) AF: 0.215 AC: 1240 AN: 5764

European-Non Finnish (NFE) AF: 0.179 AC: 198772 AN: 1111296

Other (OTH) AF: 0.231 AC: 13964 AN: 60340

GnomAD4 genome AF: 0.194 AC: 29534 AN: 152092 Hom.: 4396 Cov.: 33 AF XY: 0.208 AC XY: 15452 AN XY: 74330

African (AFR) AF: 0.0458 AC: 1902 AN: 41536

American (AMR) AF: 0.382 AC: 5842 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.305 AC: 1058 AN: 3468

East Asian (EAS) AF: 0.670 AC: 3429 AN: 5118

South Asian (SAS) AF: 0.294 AC: 1414 AN: 4810

European-Finnish (FIN) AF: 0.272 AC: 2878 AN: 10576

Middle Eastern (MID) AF: 0.214 AC: 63 AN: 294

European-Non Finnish (NFE) AF: 0.179 AC: 12202 AN: 67982

Other (OTH) AF: 0.243 AC: 512 AN: 2110

Alfa AF: 0.176 Hom.: 358

Bravo AF: 0.199

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.34
CADD	Benign	19
DANN	Benign	0.89
PhyloP100		6.6

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs13415770;

hg19: chr2-132258593;