chr10-79952597-A-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000444384.3(SFTPD):​c.37-5935T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.146 in 152,066 control chromosomes in the GnomAD database, including 2,068 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 0.15 ( 2068 hom., cov: 32)

Consequence

SFTPD
ENST00000444384.3 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.502
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]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-1.01).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.397 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
SFTPDXM_011540087.2 linkuse as main transcriptc.-3-5935T>C intron_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
SFTPDENST00000444384.3 linkuse as main transcriptc.37-5935T>C intron_variant 3

Frequencies

GnomAD3 genomes
AF:
0.146
AC:
22227
AN:
151948
Hom.:
2059
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.166
Gnomad AMI
AF:
0.0551
Gnomad AMR
AF:
0.219
Gnomad ASJ
AF:
0.150
Gnomad EAS
AF:
0.412
Gnomad SAS
AF:
0.305
Gnomad FIN
AF:
0.0617
Gnomad MID
AF:
0.172
Gnomad NFE
AF:
0.101
Gnomad OTH
AF:
0.152
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.146
AC:
22274
AN:
152066
Hom.:
2068
Cov.:
32
AF XY:
0.151
AC XY:
11221
AN XY:
74326
show subpopulations
Gnomad4 AFR
AF:
0.166
Gnomad4 AMR
AF:
0.219
Gnomad4 ASJ
AF:
0.150
Gnomad4 EAS
AF:
0.411
Gnomad4 SAS
AF:
0.305
Gnomad4 FIN
AF:
0.0617
Gnomad4 NFE
AF:
0.101
Gnomad4 OTH
AF:
0.158
Alfa
AF:
0.121
Hom.:
644
Bravo
AF:
0.158
Asia WGS
AF:
0.322
AC:
1118
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-1.0
CADD
Benign
1.4
DANN
Benign
0.44

Splicing

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.

Other links and lift over

dbSNP: rs1885551; hg19: chr10-81712353; API