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. Variant got -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

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

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SFTPD	XM_011540087.2	c.-4+2054G>T		intron_variant	Intron 1 of 7		XP_011538389.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SFTPD	ENST00000444384.3	c.36+2411G>T		intron_variant	Intron 1 of 5	3		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

Gnomad4 AFR AF: 0.844

Gnomad4 AMR AF: 0.623

Gnomad4 ASJ AF: 0.620

Gnomad4 EAS AF: 0.616

Gnomad4 SAS AF: 0.744

Gnomad4 FIN AF: 0.551

Gnomad4 NFE AF: 0.590

Gnomad4 OTH AF: 0.661

Alfa AF: 0.605 Hom.: 37026

Bravo AF: 0.676

Asia WGS AF: 0.717 AC: 2494 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11201011; hg19: chr10-81739920;