rs2181204

Variant names:

• chr10-79944756-A-G
• rs2181204
• NM_003019.5:c.199+1705T>C

Your query was ambiguous. Multiple possible variants found:

• chr10-79944756-A-G
• chr10-79944756-A-T

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+1705T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.181 in 152,028 control chromosomes in the GnomAD database, including 3,208 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 0.18 (3208 hom., cov: 32)
• Consequence: SFTPD NM_003019.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.47
• 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=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.394 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.199+1705T>C		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.199+1705T>C		intron	N/A	ENSP00000361366.3
	SFTPD	ENST00000679234.1		n.191T>C		non_coding_transcript_exon	Exon 1 of 5
	SFTPD	ENST00000444384.3	TSL:3	c.238+1705T>C		intron	N/A	ENSP00000394325.1

Frequencies

GnomAD3 genomes AF: 0.181 AC: 27448 AN: 151910 Hom.: 3196 Cov.: 32

Gnomad AFR AF: 0.283

Gnomad AMI AF: 0.0548

Gnomad AMR AF: 0.233

Gnomad ASJ AF: 0.178

Gnomad EAS AF: 0.409

Gnomad SAS AF: 0.306

Gnomad FIN AF: 0.0614

Gnomad MID AF: 0.187

Gnomad NFE AF: 0.102

Gnomad OTH AF: 0.173

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

GnomAD4 genome AF: 0.181 AC: 27506 AN: 152028 Hom.: 3208 Cov.: 32 AF XY: 0.184 AC XY: 13681 AN XY: 74320

African (AFR) AF: 0.283 AC: 11712 AN: 41412

American (AMR) AF: 0.233 AC: 3567 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.178 AC: 616 AN: 3466

East Asian (EAS) AF: 0.408 AC: 2101 AN: 5144

South Asian (SAS) AF: 0.306 AC: 1474 AN: 4818

European-Finnish (FIN) AF: 0.0614 AC: 652 AN: 10612

Middle Eastern (MID) AF: 0.187 AC: 55 AN: 294

European-Non Finnish (NFE) AF: 0.102 AC: 6902 AN: 67972

Other (OTH) AF: 0.179 AC: 377 AN: 2108

Alfa AF: 0.139 Hom.: 881

Bravo AF: 0.198

Asia WGS AF: 0.332 AC: 1152 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.13
DANN	Benign	0.67
PhyloP100		-1.5
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: rs2181204; hg19: chr10-81704512;