Genetic Variant SFTPD:c.36+6350T>C (chr10-79976225-A-G) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000444384.3(SFTPD):c.36+6350T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.06 in 152,150 control chromosomes in the GnomAD database, including 595 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 0.060 ( 595 hom., cov: 32)

Consequence

SFTPD
ENST00000444384.3 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.0970

Publications

9 publications found

Variant links:

Genes affected

SFTPD (HGNC:10803): (surfactant protein D) The protein encoded by this gene is part of the innate immune response, protecting the lungs against inhaled microorganisms and chemicals. The encoded protein may also be involved in surfactant metabolism. [provided by RefSeq, Jul 2015]

SFTPD links:

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ACMG classification

Classification was made for transcript

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

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.95).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.378 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SFTPD	XM_011540087.2 link	c.-4+5993T>C		intron_variant	Intron 1 of 7		XP_011538389.1	P35247

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SFTPD	ENST00000444384.3 link	c.36+6350T>C		intron_variant	Intron 1 of 5	3		ENSP00000394325.1		Q5T0M2

Frequencies

GnomAD3 genomes

AF:

0.0599

AC:

9103

AN:

152032

Hom.:

595

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0756

Gnomad AMI

AF:

0.0462

Gnomad AMR

AF:

0.0414

Gnomad ASJ

AF:

0.0720

Gnomad EAS

AF:

0.392

Gnomad SAS

AF:

0.104

Gnomad FIN

AF:

0.0133

Gnomad MID

AF:

0.0955

Gnomad NFE

AF:

0.0329

Gnomad OTH

AF:

0.0555

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

GnomAD4 genome

AF:

0.0600

AC:

9122

AN:

152150

Hom.:

595

Cov.:

AF XY:

0.0620

AC XY:

4614

AN XY:

74388

show subpopulations

African (AFR)

AF:

0.0759

AC:

3151

AN:

41504

American (AMR)

AF:

0.0414

AC:

632

AN:

15284

Ashkenazi Jewish (ASJ)

AF:

0.0720

AC:

250

AN:

3472

East Asian (EAS)

AF:

0.392

AC:

2018

AN:

5148

South Asian (SAS)

AF:

0.104

AC:

501

AN:

4814

European-Finnish (FIN)

AF:

0.0133

AC:

141

AN:

10608

Middle Eastern (MID)

AF:

0.0890

AC:

AN:

292

European-Non Finnish (NFE)

AF:

0.0329

AC:

2239

AN:

68006

Other (OTH)

AF:

0.0578

AC:

122

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

408

817

1225

1634

2042

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Alfa

AF:

0.0506

Hom.:

1063

Bravo

AF:

0.0641

Asia WGS

AF:

0.193

AC:

668

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.95

CADD

Benign

3.1

(source)

DANN

Benign

0.70

PhyloP100

-0.097

Splicing

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

Publications

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chr10-79976225-A-G

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over