NM_003019.5:c.199+1658T>C

Variant names:

• chr10-79944803-A-G
• rs2255601
• NM_003019.5:c.199+1658T>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_003019.5(SFTPD):​c.199+1658T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.658 in 151,834 control chromosomes in the GnomAD database, including 33,630 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 0.66 (33630 hom., cov: 30)
• Consequence: SFTPD NM_003019.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.667
• Publications: 9 publications found

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]

ENSG00000283913 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.807 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SFTPD	NM_003019.5	c.199+1658T>C		intron_variant	Intron 2 of 7	ENST00000372292.8	NP_003010.4
SFTPD	XM_011540087.2	c.199+1658T>C		intron_variant	Intron 2 of 7		XP_011538389.1
SFTPD	XM_011540088.3	c.199+1658T>C		intron_variant	Intron 2 of 6		XP_011538390.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SFTPD	ENST00000372292.8	c.199+1658T>C		intron_variant	Intron 2 of 7	1	NM_003019.5	ENSP00000361366.3

Frequencies

GnomAD3 genomes AF: 0.657 AC: 99735 AN: 151716 Hom.: 33577 Cov.: 30

Gnomad AFR AF: 0.814

Gnomad AMI AF: 0.650

Gnomad AMR AF: 0.615

Gnomad ASJ AF: 0.608

Gnomad EAS AF: 0.615

Gnomad SAS AF: 0.735

Gnomad FIN AF: 0.552

Gnomad MID AF: 0.703

Gnomad NFE AF: 0.588

Gnomad OTH AF: 0.646

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

GnomAD4 genome AF: 0.658 AC: 99849 AN: 151834 Hom.: 33630 Cov.: 30 AF XY: 0.657 AC XY: 48741 AN XY: 74166

African (AFR) AF: 0.814 AC: 33734 AN: 41436

American (AMR) AF: 0.615 AC: 9395 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.608 AC: 2105 AN: 3462

East Asian (EAS) AF: 0.614 AC: 3156 AN: 5136

South Asian (SAS) AF: 0.736 AC: 3536 AN: 4806

European-Finnish (FIN) AF: 0.552 AC: 5804 AN: 10508

Middle Eastern (MID) AF: 0.697 AC: 205 AN: 294

European-Non Finnish (NFE) AF: 0.588 AC: 39949 AN: 67902

Other (OTH) AF: 0.651 AC: 1375 AN: 2112

Alfa AF: 0.644 Hom.: 4482

Bravo AF: 0.665

Asia WGS AF: 0.715 AC: 2487 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.32
DANN	Benign	0.32
PhyloP100		-0.67
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs2255601; hg19: chr10-81704559;