rs1059225

Variant names:

• chr10-79615230-T-A
• rs1059225
• NM_005411.5:c.*1117T>A

Your query was ambiguous. Multiple possible variants found:

• chr10-79615230-T-A
• chr10-79615230-T-C
• chr10-79615230-T-G

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_001093770.3(SFTPA1):​c.*1117T>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 31)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: SFTPA1 NM_001093770.3 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0740
• Publications: 7 publications found

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]

ACMG classification

Our verdict: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001093770.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SFTPA1	NM_005411.5	MANE Select	c.*1117T>A		3_prime_UTR	Exon 6 of 6	NP_005402.3
	SFTPA1	NM_001093770.3		c.*1117T>A		3_prime_UTR	Exon 6 of 6	NP_001087239.2
	SFTPA1	NM_001164644.2		c.*1117T>A		3_prime_UTR	Exon 6 of 6	NP_001158116.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SFTPA1	ENST00000398636.8	TSL:1 MANE Select	c.*1117T>A		3_prime_UTR	Exon 6 of 6	ENSP00000381633.3
	SFTPA1	ENST00000419470.6	TSL:1	c.*1117T>A		3_prime_UTR	Exon 6 of 6	ENSP00000397082.2
	SFTPA1	ENST00000428376.6	TSL:1	c.*1117T>A		3_prime_UTR	Exon 5 of 5	ENSP00000411102.2

Frequencies

GnomAD3 genomes Cov.: 31

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 311472 Hom.: 0 Cov.: 6 AF XY: 0.00 AC XY: 0 AN XY: 161582

African (AFR) AF: 0.00 AC: 0 AN: 6894

American (AMR) AF: 0.00 AC: 0 AN: 8162

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 4586

East Asian (EAS) AF: 0.00 AC: 0 AN: 7448

South Asian (SAS) AF: 0.00 AC: 0 AN: 36224

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 23198

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 888

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 211862

Other (OTH) AF: 0.00 AC: 0 AN: 12210

GnomAD4 genome Cov.: 31

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	1.5
DANN	Benign	0.79
PhyloP100		-0.074

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.020		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: rs1059225; hg19: chr10-81374986;