10-79557057-G-A

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_Strong BP6_Moderate BA1

The NM_001098668.4(SFTPA2):c.*152C>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0755 in 1,265,498 control chromosomes in the GnomAD database, including 4,523 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.073 (559 hom., cov: 32)
  • Exomes 𝑓: 0.076 (3964 hom.)
• Consequence: SFTPA2 NM_001098668.4 3_prime_UTR
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 0.0530

Genes affected

SFTPA2 (HGNC:10799): (surfactant protein A2) This gene is one of several genes encoding pulmonary-surfactant associated proteins (SFTPA) located on chromosome 10. Mutations in this gene and a highly similar gene located nearby, which affect the highly conserved carbohydrate recognition domain, are associated with idiopathic pulmonary fibrosis. The current version of the assembly displays only a single centromeric SFTPA gene pair rather than the two gene pairs shown in the previous assembly which were thought to have resulted from a duplication. [provided by RefSeq, Sep 2009]

ACMG classification

Verdict is Benign. Variant got -14 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BP6: Variant 10-79557057-G-A is Benign according to our data. Variant chr10-79557057-G-A is described in ClinVar as [Benign]. Clinvar id is 1258839.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.271 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SFTPA2	NM_001098668.4	c.*152C>T		3_prime_UTR_variant	6/6	ENST00000372325.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SFTPA2	ENST00000372325.7	c.*152C>T		3_prime_UTR_variant	6/6	1	NM_001098668.4	P1

Frequencies

GnomAD3 genomes AF: 0.0731 AC: 11106 AN: 151978 Hom.: 558 Cov.: 32

Gnomad AFR AF: 0.0409

Gnomad AMI AF: 0.103

Gnomad AMR AF: 0.0673

Gnomad ASJ AF: 0.0916

Gnomad EAS AF: 0.283

Gnomad SAS AF: 0.0704

Gnomad FIN AF: 0.0728

Gnomad MID AF: 0.0949

Gnomad NFE AF: 0.0766

Gnomad OTH AF: 0.0807

GnomAD4 exome AF: 0.0759 AC: 84464 AN: 1113402 Hom.: 3964 Cov.: 16 AF XY: 0.0756 AC XY: 41862 AN XY: 553626

Gnomad4 AFR exome AF: 0.0392

Gnomad4 AMR exome AF: 0.0446

Gnomad4 ASJ exome AF: 0.0905

Gnomad4 EAS exome AF: 0.247

Gnomad4 SAS exome AF: 0.0663

Gnomad4 FIN exome AF: 0.0787

Gnomad4 NFE exome AF: 0.0709

Gnomad4 OTH exome AF: 0.0851

GnomAD4 genome AF: 0.0732 AC: 11131 AN: 152096 Hom.: 559 Cov.: 32 AF XY: 0.0745 AC XY: 5541 AN XY: 74348

Gnomad4 AFR AF: 0.0411

Gnomad4 AMR AF: 0.0673

Gnomad4 ASJ AF: 0.0916

Gnomad4 EAS AF: 0.284

Gnomad4 SAS AF: 0.0710

Gnomad4 FIN AF: 0.0728

Gnomad4 NFE AF: 0.0766

Gnomad4 OTH AF: 0.0841

Alfa AF: 0.0706 Hom.: 58

Bravo AF: 0.0723

Asia WGS AF: 0.177 AC: 614 AN: 3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Nov 12, 2018

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Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
Cadd	Benign	1.3
Dann	Benign	0.44

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

Publications

LitVar

Other links and lift over

dbSNP: rs9408; hg19: chr10-81316813; COSMIC: COSV64882393; COSMIC: COSV64882393;