chr10-79949523-C-T

Variant names:

• chr10-79949523-C-T
• rs12219080
• ENST00000444384.3:c.37-2861G>A

Variant summary

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

The ENST00000444384.3(SFTPD):​c.37-2861G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0891 in 152,204 control chromosomes in the GnomAD database, including 1,169 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 0.089 (1169 hom., cov: 32)
• Consequence: SFTPD ENST00000444384.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0290
• Publications: 4 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=-0.65).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.378 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SFTPD	XM_011540087.2	c.-3-2861G>A		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.37-2861G>A		intron_variant	Intron 1 of 5	3		ENSP00000394325.1
ENSG00000283913	ENST00000421889.1	n.334-505C>T		intron_variant	Intron 3 of 3	3
ENSG00000283913	ENST00000453174.7	n.962-505C>T		intron_variant	Intron 7 of 7	2

Frequencies

GnomAD3 genomes AF: 0.0891 AC: 13550 AN: 152086 Hom.: 1169 Cov.: 32

Gnomad AFR AF: 0.177

Gnomad AMI AF: 0.0461

Gnomad AMR AF: 0.0524

Gnomad ASJ AF: 0.0718

Gnomad EAS AF: 0.393

Gnomad SAS AF: 0.104

Gnomad FIN AF: 0.0133

Gnomad MID AF: 0.0981

Gnomad NFE AF: 0.0333

Gnomad OTH AF: 0.0737

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

GnomAD4 genome AF: 0.0891 AC: 13568 AN: 152204 Hom.: 1169 Cov.: 32 AF XY: 0.0898 AC XY: 6685 AN XY: 74426

African (AFR) AF: 0.177 AC: 7352 AN: 41498

American (AMR) AF: 0.0523 AC: 800 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.0718 AC: 249 AN: 3470

East Asian (EAS) AF: 0.393 AC: 2027 AN: 5162

South Asian (SAS) AF: 0.105 AC: 505 AN: 4828

European-Finnish (FIN) AF: 0.0133 AC: 141 AN: 10616

Middle Eastern (MID) AF: 0.0918 AC: 27 AN: 294

European-Non Finnish (NFE) AF: 0.0333 AC: 2264 AN: 68012

Other (OTH) AF: 0.0762 AC: 161 AN: 2112

Alfa AF: 0.0752 Hom.: 156

Bravo AF: 0.0968

Asia WGS AF: 0.200 AC: 695 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.65
CADD	Benign	11
DANN	Benign	0.78
PhyloP100		0.029
PromoterAI		-0.093	Neutral

Splicing

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

Other links and lift over

dbSNP: rs12219080; hg19: chr10-81709279;