Variant chr10-79557057-G-A details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

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

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: 0.0530

Variant links:

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]

SFTPA2 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 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_multiple_submitters_no_conflicts, 2 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 linkuse as main transcript	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 linkuse as main transcript	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.:

show subpopulations

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.:

AF XY:

0.0756

AC XY:

41862

AN XY:

553626

show subpopulations

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.:

AF XY:

0.0745

AC XY:

5541

AN XY:

74348

show subpopulations

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.:

Bravo

AF:

0.0723

Asia WGS

AF:

0.177

AC:

614

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Benign, criteria provided, single submitter	clinical testing	GeneDx	Nov 12, 2018	- -
Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -

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

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over