10-79947857-A-C

Variant names:

• chr10-79947857-A-C
• rs2819096
• NM_003019.5:c.-3-1195T>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.-3-1195T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.627 in 152,084 control chromosomes in the GnomAD database, including 30,443 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 0.63 (30443 hom., cov: 32)
• Consequence: SFTPD NM_003019.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.174
• Publications: 11 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 (AFR) allele frequency at 95% confidence interval = 0.74 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SFTPD	NM_003019.5	c.-3-1195T>G		intron_variant	Intron 1 of 7	ENST00000372292.8	NP_003010.4
SFTPD	XM_011540087.2	c.-3-1195T>G		intron_variant	Intron 1 of 7		XP_011538389.1
SFTPD	XM_011540088.3	c.-3-1195T>G		intron_variant	Intron 1 of 6		XP_011538390.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SFTPD	ENST00000372292.8	c.-3-1195T>G		intron_variant	Intron 1 of 7	1	NM_003019.5	ENSP00000361366.3

Frequencies

GnomAD3 genomes AF: 0.627 AC: 95312 AN: 151966 Hom.: 30396 Cov.: 32

Gnomad AFR AF: 0.747

Gnomad AMI AF: 0.648

Gnomad AMR AF: 0.588

Gnomad ASJ AF: 0.588

Gnomad EAS AF: 0.615

Gnomad SAS AF: 0.727

Gnomad FIN AF: 0.550

Gnomad MID AF: 0.658

Gnomad NFE AF: 0.571

Gnomad OTH AF: 0.612

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

GnomAD4 genome AF: 0.627 AC: 95422 AN: 152084 Hom.: 30443 Cov.: 32 AF XY: 0.627 AC XY: 46647 AN XY: 74338

African (AFR) AF: 0.747 AC: 30991 AN: 41502

American (AMR) AF: 0.588 AC: 8982 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.588 AC: 2040 AN: 3472

East Asian (EAS) AF: 0.614 AC: 3169 AN: 5158

South Asian (SAS) AF: 0.727 AC: 3508 AN: 4824

European-Finnish (FIN) AF: 0.550 AC: 5812 AN: 10568

Middle Eastern (MID) AF: 0.656 AC: 193 AN: 294

European-Non Finnish (NFE) AF: 0.571 AC: 38836 AN: 67964

Other (OTH) AF: 0.617 AC: 1301 AN: 2108

Alfa AF: 0.587 Hom.: 43805

Bravo AF: 0.632

Asia WGS AF: 0.705 AC: 2453 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	5.8
DANN	Benign	0.38
PhyloP100		-0.17
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.040		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: rs2819096; hg19: chr10-81707613;