Variant chr10-79611665-A-T 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_005411.5(SFTPA1):c.-23-138A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.088 in 1,552,272 control chromosomes in the GnomAD database, including 7,473 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.11 ( 1087 hom., cov: 33)

Exomes 𝑓: 0.085 ( 6386 hom. )

Consequence

SFTPA1
NM_005411.5 intron

Scores

Clinical Significance

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

Conservation

PhyloP100: -1.22

Variant links:

Genes affected

SFTPA1 (HGNC:10798): (surfactant protein A1) This gene encodes a lung surfactant protein that is a member of a subfamily of C-type lectins called collectins. The encoded protein binds specific carbohydrate moieties found on lipids and on the surface of microorganisms. This protein plays an essential role in surfactant homeostasis and in the defense against respiratory pathogens. Mutations in this gene are associated with idiopathic pulmonary fibrosis. Alternate splicing results in multiple transcript variants. [provided by RefSeq, May 2010]

SFTPA1 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-1.0).

BP6

Variant 10-79611665-A-T is Benign according to our data. Variant chr10-79611665-A-T is described in ClinVar as [Benign]. Clinvar id is 1260769.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.229 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SFTPA1	NM_005411.5 linkuse as main transcript	c.-23-138A>T		intron_variant		ENST00000398636.8	NP_005402.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SFTPA1	ENST00000398636.8 linkuse as main transcript	c.-23-138A>T		intron_variant		1	NM_005411.5	ENSP00000381633	P1	Q8IWL2-1

Frequencies

GnomAD3 genomes

AF:

0.112

AC:

16939

AN:

151912

Hom.:

1087

Cov.:

show subpopulations

Gnomad AFR

AF:

0.137

Gnomad AMI

AF:

0.110

Gnomad AMR

AF:

0.115

Gnomad ASJ

AF:

0.148

Gnomad EAS

AF:

0.240

Gnomad SAS

AF:

0.0740

Gnomad FIN

AF:

0.0980

Gnomad MID

AF:

0.174

Gnomad NFE

AF:

0.0877

Gnomad OTH

AF:

0.129

GnomAD3 exomes

AF:

0.0825

AC:

14492

AN:

175766

Hom.:

972

AF XY:

0.0784

AC XY:

7374

AN XY:

94106

show subpopulations

Gnomad AFR exome

AF:

0.119

Gnomad AMR exome

AF:

0.0756

Gnomad ASJ exome

AF:

0.105

Gnomad EAS exome

AF:

0.233

Gnomad SAS exome

AF:

0.0439

Gnomad FIN exome

AF:

0.0828

Gnomad NFE exome

AF:

0.0647

Gnomad OTH exome

AF:

0.0859

GnomAD4 exome

AF:

0.0855

AC:

119703

AN:

1400242

Hom.:

6386

Cov.:

AF XY:

0.0845

AC XY:

58461

AN XY:

692188

show subpopulations

Gnomad4 AFR exome

AF:

0.132

Gnomad4 AMR exome

AF:

0.0913

Gnomad4 ASJ exome

AF:

0.138

Gnomad4 EAS exome

AF:

0.219

Gnomad4 SAS exome

AF:

0.0611

Gnomad4 FIN exome

AF:

0.105

Gnomad4 NFE exome

AF:

0.0781

Gnomad4 OTH exome

AF:

0.102

GnomAD4 genome

AF:

0.112

AC:

16967

AN:

152030

Hom.:

1087

Cov.:

AF XY:

0.113

AC XY:

8411

AN XY:

74306

show subpopulations

Gnomad4 AFR

AF:

0.137

Gnomad4 AMR

AF:

0.114

Gnomad4 ASJ

AF:

0.148

Gnomad4 EAS

AF:

0.240

Gnomad4 SAS

AF:

0.0743

Gnomad4 FIN

AF:

0.0980

Gnomad4 NFE

AF:

0.0877

Gnomad4 OTH

AF:

0.131

Alfa

AF:

0.0990

Hom.:

144

Bravo

AF:

0.115

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

-1.0

CADD

Benign

1.1

DANN

Benign

0.23

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.040

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