1-153071533-G-A

Variant names:

• chr1-153071533-G-A
• rs6693927
• NM_001388198.1:c.-20+36C>T

Variant summary

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

The NM_001388198.1(SPRR2B):​c.-20+36C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.352 in 151,836 control chromosomes in the GnomAD database, including 10,376 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 0.35 (10376 hom., cov: 31)
• Consequence: SPRR2B NM_001388198.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0670
• Publications: 9 publications found

Genes affected

SPRR2B (HGNC:11262): (small proline rich protein 2B) Predicted to be involved in keratinization. Predicted to act upstream of or within response to estradiol. Predicted to be located in cornified envelope and cytosol. [provided by Alliance of Genome Resources, Apr 2022]

ENSG00000301557 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.45 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001388198.1. 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
	SPRR2B	NM_001388198.1	MANE Select	c.-20+36C>T		intron	N/A	NP_001375127.1
	SPRR2B	NM_001017418.3		c.-20+32C>T		intron	N/A	NP_001017418.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SPRR2B	ENST00000368755.3	TSL:6 MANE Select	c.-20+36C>T		intron	N/A	ENSP00000357744.1
	ENSG00000301557	ENST00000779687.1		n.138+963G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.353 AC: 53489 AN: 151718 Hom.: 10375 Cov.: 31

Gnomad AFR AF: 0.221

Gnomad AMI AF: 0.363

Gnomad AMR AF: 0.292

Gnomad ASJ AF: 0.481

Gnomad EAS AF: 0.171

Gnomad SAS AF: 0.259

Gnomad FIN AF: 0.383

Gnomad MID AF: 0.367

Gnomad NFE AF: 0.454

Gnomad OTH AF: 0.372

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.352 AC: 53503 AN: 151836 Hom.: 10376 Cov.: 31 AF XY: 0.347 AC XY: 25719 AN XY: 74210

African (AFR) AF: 0.221 AC: 9143 AN: 41400

American (AMR) AF: 0.292 AC: 4451 AN: 15244

Ashkenazi Jewish (ASJ) AF: 0.481 AC: 1667 AN: 3466

East Asian (EAS) AF: 0.171 AC: 884 AN: 5158

South Asian (SAS) AF: 0.259 AC: 1244 AN: 4802

European-Finnish (FIN) AF: 0.383 AC: 4027 AN: 10514

Middle Eastern (MID) AF: 0.374 AC: 110 AN: 294

European-Non Finnish (NFE) AF: 0.454 AC: 30872 AN: 67942

Other (OTH) AF: 0.368 AC: 775 AN: 2108

Alfa AF: 0.416 Hom.: 12262

Bravo AF: 0.340

Asia WGS AF: 0.204 AC: 709 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	4.7
DANN	Benign	0.64
PhyloP100		-0.067
PromoterAI		-0.010	Neutral
Mutation Taster		=100/0	polymorphism (auto)

Splicing

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

Other links and lift over

dbSNP: rs6693927; hg19: chr1-153044009;