chr1-153003830-T-G

Variant names:

• chr1-153003830-T-G
• rs1134220
• NM_001097589.2:c.*300T>G

Variant summary

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

The NM_001097589.2(SPRR3):​c.*300T>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 0.536 in 438,488 control chromosomes in the GnomAD database, including 64,140 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 0.53 (21531 hom., cov: 32)
  • Exomes 𝑓: 0.54 (42609 hom.)
• Consequence: SPRR3 NM_001097589.2 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.00
• Publications: 5 publications found

Genes affected

SPRR3 (HGNC:11268): (small proline rich protein 3) Predicted to enable structural molecule activity. Predicted to be involved in wound healing. Located in Golgi apparatus and perinuclear region of cytoplasm. [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=-0.79).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.634 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SPRR3	NM_001097589.2	c.*300T>G		3_prime_UTR_variant	Exon 2 of 2	ENST00000295367.5	NP_001091058.1
SPRR3	NM_005416.3	c.*300T>G		3_prime_UTR_variant	Exon 3 of 3		NP_005407.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SPRR3	ENST00000295367.5	c.*300T>G		3_prime_UTR_variant	Exon 2 of 2	1	NM_001097589.2	ENSP00000295367.4
SPRR3	ENST00000331860.7	c.*300T>G		3_prime_UTR_variant	Exon 3 of 3	3		ENSP00000330391.3

Frequencies

GnomAD3 genomes AF: 0.530 AC: 80565 AN: 151900 Hom.: 21505 Cov.: 32

Gnomad AFR AF: 0.515

Gnomad AMI AF: 0.438

Gnomad AMR AF: 0.484

Gnomad ASJ AF: 0.570

Gnomad EAS AF: 0.653

Gnomad SAS AF: 0.523

Gnomad FIN AF: 0.509

Gnomad MID AF: 0.513

Gnomad NFE AF: 0.544

Gnomad OTH AF: 0.527

GnomAD4 exome AF: 0.539 AC: 154537 AN: 286470 Hom.: 42609 Cov.: 3 AF XY: 0.540 AC XY: 80085 AN XY: 148392

African (AFR) AF: 0.515 AC: 4691 AN: 9110

American (AMR) AF: 0.469 AC: 4959 AN: 10564

Ashkenazi Jewish (ASJ) AF: 0.568 AC: 5007 AN: 8810

East Asian (EAS) AF: 0.659 AC: 11920 AN: 18076

South Asian (SAS) AF: 0.519 AC: 13022 AN: 25078

European-Finnish (FIN) AF: 0.513 AC: 14925 AN: 29120

Middle Eastern (MID) AF: 0.466 AC: 571 AN: 1226

European-Non Finnish (NFE) AF: 0.540 AC: 90838 AN: 168246

Other (OTH) AF: 0.530 AC: 8604 AN: 16240

GnomAD4 genome AF: 0.530 AC: 80643 AN: 152018 Hom.: 21531 Cov.: 32 AF XY: 0.527 AC XY: 39181 AN XY: 74332

African (AFR) AF: 0.515 AC: 21351 AN: 41454

American (AMR) AF: 0.484 AC: 7405 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.570 AC: 1978 AN: 3470

East Asian (EAS) AF: 0.653 AC: 3367 AN: 5160

South Asian (SAS) AF: 0.523 AC: 2520 AN: 4818

European-Finnish (FIN) AF: 0.509 AC: 5378 AN: 10566

Middle Eastern (MID) AF: 0.517 AC: 152 AN: 294

European-Non Finnish (NFE) AF: 0.544 AC: 36984 AN: 67952

Other (OTH) AF: 0.527 AC: 1110 AN: 2108

Alfa AF: 0.536 Hom.: 6637

Bravo AF: 0.530

Asia WGS AF: 0.547 AC: 1903 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	2.1
DANN	Benign	0.82
PhyloP100		-2.0
Mutation Taster		=100/0	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: rs1134220; hg19: chr1-152976306;