10-79943078-T-C

Variant names:

• chr10-79943078-T-C
• rs10887199
• NM_003019.5:c.200-199A>G

Variant summary

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

The NM_003019.5(SFTPD):​c.200-199A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.182 in 151,880 control chromosomes in the GnomAD database, including 3,227 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as (no stars).

• Frequency: Genomes: 𝑓 0.18 (3227 hom., cov: 32)
• Consequence: SFTPD NM_003019.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.43
• Publications: 12 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=-0.99).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.395 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_003019.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SFTPD	NM_003019.5	MANE Select	c.200-199A>G		intron	N/A	NP_003010.4

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SFTPD	ENST00000372292.8	TSL:1 MANE Select	c.200-199A>G		intron	N/A	ENSP00000361366.3
	SFTPD	ENST00000946714.1		c.368-199A>G		intron	N/A	ENSP00000616773.1
	SFTPD	ENST00000946710.1		c.341-199A>G		intron	N/A	ENSP00000616769.1

Frequencies

GnomAD3 genomes AF: 0.182 AC: 27596 AN: 151764 Hom.: 3214 Cov.: 32

Gnomad AFR AF: 0.286

Gnomad AMI AF: 0.0549

Gnomad AMR AF: 0.234

Gnomad ASJ AF: 0.173

Gnomad EAS AF: 0.409

Gnomad SAS AF: 0.306

Gnomad FIN AF: 0.0619

Gnomad MID AF: 0.193

Gnomad NFE AF: 0.102

Gnomad OTH AF: 0.174

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

GnomAD4 genome AF: 0.182 AC: 27658 AN: 151880 Hom.: 3227 Cov.: 32 AF XY: 0.185 AC XY: 13768 AN XY: 74224

African (AFR) AF: 0.287 AC: 11859 AN: 41384

American (AMR) AF: 0.234 AC: 3573 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.173 AC: 601 AN: 3470

East Asian (EAS) AF: 0.409 AC: 2098 AN: 5126

South Asian (SAS) AF: 0.306 AC: 1467 AN: 4798

European-Finnish (FIN) AF: 0.0619 AC: 654 AN: 10568

Middle Eastern (MID) AF: 0.194 AC: 57 AN: 294

European-Non Finnish (NFE) AF: 0.102 AC: 6920 AN: 67962

Other (OTH) AF: 0.180 AC: 379 AN: 2108

Alfa AF: 0.131 Hom.: 2064

Bravo AF: 0.199

Asia WGS AF: 0.331 AC: 1149 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.048
DANN	Benign	0.47
PhyloP100		-2.4
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: rs10887199; hg19: chr10-81702834; COSMIC: COSV107466472;