rs11201011

Variant names:

• chr10-79980164-C-A
• rs11201011
• ENST00000444384.3:c.36+2411G>T

Your query was ambiguous. Multiple possible variants found:

• chr10-79980164-C-A
• chr10-79980164-C-G

Variant summary

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

The ENST00000444384.3(SFTPD):​c.36+2411G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.668 in 151,952 control chromosomes in the GnomAD database, including 34,872 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 0.67 (34872 hom., cov: 32)
• Consequence: SFTPD ENST00000444384.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.698
• Publications: 10 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]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.836 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000444384.3. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SFTPD	ENST00000444384.3	TSL:3	c.36+2411G>T		intron	N/A	ENSP00000394325.1

Frequencies

GnomAD3 genomes AF: 0.667 AC: 101322 AN: 151834 Hom.: 34812 Cov.: 32

Gnomad AFR AF: 0.843

Gnomad AMI AF: 0.625

Gnomad AMR AF: 0.623

Gnomad ASJ AF: 0.620

Gnomad EAS AF: 0.616

Gnomad SAS AF: 0.743

Gnomad FIN AF: 0.551

Gnomad MID AF: 0.718

Gnomad NFE AF: 0.590

Gnomad OTH AF: 0.656

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

GnomAD4 genome AF: 0.668 AC: 101443 AN: 151952 Hom.: 34872 Cov.: 32 AF XY: 0.667 AC XY: 49518 AN XY: 74236

African (AFR) AF: 0.844 AC: 34989 AN: 41468

American (AMR) AF: 0.623 AC: 9515 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.620 AC: 2148 AN: 3462

East Asian (EAS) AF: 0.616 AC: 3172 AN: 5152

South Asian (SAS) AF: 0.744 AC: 3568 AN: 4798

European-Finnish (FIN) AF: 0.551 AC: 5794 AN: 10524

Middle Eastern (MID) AF: 0.714 AC: 210 AN: 294

European-Non Finnish (NFE) AF: 0.590 AC: 40082 AN: 67960

Other (OTH) AF: 0.661 AC: 1396 AN: 2112

Alfa AF: 0.627 Hom.: 58437

Bravo AF: 0.676

Asia WGS AF: 0.717 AC: 2494 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.54
DANN	Benign	0.14
PhyloP100		-0.70

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs11201011; hg19: chr10-81739920;