3-150542155-T-C

Variant names:

• chr3-150542155-T-C
• rs8052
• NM_014445.4:c.*2303A>G

Variant summary

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

The NM_014445.4(SERP1):​c.*2303A>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.82 in 152,200 control chromosomes in the GnomAD database, including 51,706 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 0.82 (51705 hom., cov: 33)
  • Exomes 𝑓: 1.0 (1 hom.)
• Consequence: SERP1 NM_014445.4 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0630
• Publications: 9 publications found

Genes affected

SERP1 (HGNC:10759): (stress associated endoplasmic reticulum protein 1) Predicted to be involved in endoplasmic reticulum unfolded protein response and protein glycosylation. Predicted to act upstream of or within several processes, including multicellular organism aging; positive regulation of organ growth; and positive regulation of peptide hormone secretion. Located in cytoplasmic microtubule. [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=-0.83).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.888 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SERP1	NM_014445.4	c.*2303A>G		3_prime_UTR_variant	Exon 3 of 3	ENST00000239944.7	NP_055260.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SERP1	ENST00000239944.7	c.*2303A>G		3_prime_UTR_variant	Exon 3 of 3	1	NM_014445.4	ENSP00000239944.2
SERP1	ENST00000479209.1	c.*2303A>G		3_prime_UTR_variant	Exon 4 of 4	2		ENSP00000420076.1

Frequencies

GnomAD3 genomes AF: 0.820 AC: 124659 AN: 152080 Hom.: 51672 Cov.: 33

Gnomad AFR AF: 0.686

Gnomad AMI AF: 0.860

Gnomad AMR AF: 0.833

Gnomad ASJ AF: 0.839

Gnomad EAS AF: 0.910

Gnomad SAS AF: 0.892

Gnomad FIN AF: 0.889

Gnomad MID AF: 0.823

Gnomad NFE AF: 0.874

Gnomad OTH AF: 0.816

GnomAD4 exome AF: 1.00 AC: 2 AN: 2 Hom.: 1 Cov.: 0 AF XY: 1.00 AC XY: 2 AN XY: 2

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AC: 0 AN: 0

Middle Eastern (MID) AF: 1.00 AC: 2 AN: 2

European-Non Finnish (NFE) AC: 0 AN: 0

Other (OTH) AC: 0 AN: 0

GnomAD4 genome AF: 0.820 AC: 124749 AN: 152198 Hom.: 51705 Cov.: 33 AF XY: 0.824 AC XY: 61304 AN XY: 74392

African (AFR) AF: 0.687 AC: 28477 AN: 41480

American (AMR) AF: 0.833 AC: 12740 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.839 AC: 2910 AN: 3470

East Asian (EAS) AF: 0.910 AC: 4724 AN: 5192

South Asian (SAS) AF: 0.892 AC: 4303 AN: 4826

European-Finnish (FIN) AF: 0.889 AC: 9414 AN: 10594

Middle Eastern (MID) AF: 0.827 AC: 243 AN: 294

European-Non Finnish (NFE) AF: 0.874 AC: 59432 AN: 68018

Other (OTH) AF: 0.816 AC: 1723 AN: 2112

Alfa AF: 0.854 Hom.: 73417

Bravo AF: 0.807

Asia WGS AF: 0.853 AC: 2970 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	9.5
DANN	Benign	0.87
PhyloP100		-0.063
Mutation Taster		=99/1	polymorphism (auto)

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: rs8052; hg19: chr3-150259942;