1-67419714-G-C

Variant names:

• chr1-67419714-G-C
• rs3790557
• NM_001018069.2:c.951+295C>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The NM_001018069.2(SERBP1):​c.951+295C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00592 in 288,510 control chromosomes in the GnomAD database, including 25 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 0.0059 (13 hom., cov: 32)
  • Exomes 𝑓: 0.0060 (12 hom.)
• Consequence: SERBP1 NM_001018069.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.10
• Publications: 1 publications found

Genes affected

SERBP1 (HGNC:17860): (SERPINE1 mRNA binding protein 1) Enables SUMO binding activity; mRNA 3'-UTR binding activity; and ribosome binding activity. Involved in PML body organization. Located in cytosol and nucleus. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BS1: Variant frequency is greater than expected in population eas. GnomAd4 allele frequency = 0.00589 (896/152164) while in subpopulation EAS AF = 0.0437 (226/5176). AF 95% confidence interval is 0.039. There are 13 homozygotes in GnomAd4. There are 440 alleles in the male GnomAd4 subpopulation. Median coverage is 32. This position passed quality control check.
• BS2: High AC in GnomAd4 at 896 AD gene.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001018069.2. 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
	SERBP1	NM_001018069.2	MANE Select	c.951+295C>G		intron	N/A	NP_001018079.1
	SERBP1	NM_001018067.2		c.996+295C>G		intron	N/A	NP_001018077.1
	SERBP1	NM_001018068.2		c.978+295C>G		intron	N/A	NP_001018078.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SERBP1	ENST00000361219.11	TSL:1 MANE Select	c.951+295C>G		intron	N/A	ENSP00000354591.6
	SERBP1	ENST00000370995.6	TSL:1	c.996+295C>G		intron	N/A	ENSP00000360034.2
	SERBP1	ENST00000370990.5	TSL:1	c.978+295C>G		intron	N/A	ENSP00000360029.5

Frequencies

GnomAD3 genomes AF: 0.00588 AC: 894 AN: 152046 Hom.: 13 Cov.: 32

Gnomad AFR AF: 0.000918

Gnomad AMI AF: 0.00877

Gnomad AMR AF: 0.0126

Gnomad ASJ AF: 0.000576

Gnomad EAS AF: 0.0434

Gnomad SAS AF: 0.000621

Gnomad FIN AF: 0.00727

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.00497

Gnomad OTH AF: 0.00526

GnomAD4 exome AF: 0.00596 AC: 812 AN: 136346 Hom.: 12 AF XY: 0.00547 AC XY: 395 AN XY: 72254

African (AFR) AF: 0.00134 AC: 4 AN: 2992

American (AMR) AF: 0.0147 AC: 74 AN: 5036

Ashkenazi Jewish (ASJ) AF: 0.00165 AC: 7 AN: 4240

East Asian (EAS) AF: 0.0418 AC: 256 AN: 6124

South Asian (SAS) AF: 0.000724 AC: 11 AN: 15192

European-Finnish (FIN) AF: 0.00576 AC: 38 AN: 6594

Middle Eastern (MID) AF: 0.00327 AC: 2 AN: 612

European-Non Finnish (NFE) AF: 0.00399 AC: 349 AN: 87386

Other (OTH) AF: 0.00869 AC: 71 AN: 8170

GnomAD4 genome AF: 0.00589 AC: 896 AN: 152164 Hom.: 13 Cov.: 32 AF XY: 0.00591 AC XY: 440 AN XY: 74400

African (AFR) AF: 0.000915 AC: 38 AN: 41524

American (AMR) AF: 0.0126 AC: 192 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.000576 AC: 2 AN: 3472

East Asian (EAS) AF: 0.0437 AC: 226 AN: 5176

South Asian (SAS) AF: 0.000622 AC: 3 AN: 4824

European-Finnish (FIN) AF: 0.00727 AC: 77 AN: 10586

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 294

European-Non Finnish (NFE) AF: 0.00497 AC: 338 AN: 67988

Other (OTH) AF: 0.00568 AC: 12 AN: 2112

Alfa AF: 0.00842 Hom.: 0

Bravo AF: 0.00605

Asia WGS AF: 0.0310 AC: 108 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	0.56
DANN	Benign	0.57
PhyloP100		-1.1
Mutation Taster		=100/0	polymorphism

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Other links and lift over

dbSNP: rs3790557; hg19: chr1-67885397;