rs1923534

Variant names:

• chr10-79950729-A-G
• rs1923534
• ENST00000453174.7:n.1663A>G

Variant summary

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

The ENST00000453174.7(ENSG00000283913):​n.1663A>G variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0694 in 152,306 control chromosomes in the GnomAD database, including 571 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 0.069 (571 hom., cov: 32)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: ENSG00000283913 ENST00000453174.7 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.347
• Publications: 6 publications found

Genes affected

ENSG00000283913 (HGNC:):

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=-0.75).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.19 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SFTPD	XM_011540087.2	c.-3-4067T>C		intron_variant	Intron 1 of 7		XP_011538389.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000283913	ENST00000453174.7	n.1663A>G		non_coding_transcript_exon_variant	Exon 8 of 8	2
ENSG00000283913	ENST00000818194.1	n.1335A>G		non_coding_transcript_exon_variant	Exon 4 of 4
SFTPD	ENST00000444384.3	c.37-4067T>C		intron_variant	Intron 1 of 5	3		ENSP00000394325.1

Frequencies

GnomAD3 genomes AF: 0.0693 AC: 10548 AN: 152188 Hom.: 564 Cov.: 32

Gnomad AFR AF: 0.0299

Gnomad AMI AF: 0.00877

Gnomad AMR AF: 0.173

Gnomad ASJ AF: 0.0784

Gnomad EAS AF: 0.0165

Gnomad SAS AF: 0.202

Gnomad FIN AF: 0.0484

Gnomad MID AF: 0.0759

Gnomad NFE AF: 0.0678

Gnomad OTH AF: 0.0860

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 2 Hom.: 0 Cov.: 0 AC XY: 0 AN XY: 0

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 2

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AC: 0 AN: 0

Other (OTH) AC: 0 AN: 0

GnomAD4 genome AF: 0.0694 AC: 10577 AN: 152306 Hom.: 571 Cov.: 32 AF XY: 0.0731 AC XY: 5441 AN XY: 74470

African (AFR) AF: 0.0300 AC: 1249 AN: 41582

American (AMR) AF: 0.174 AC: 2657 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.0784 AC: 272 AN: 3470

East Asian (EAS) AF: 0.0166 AC: 86 AN: 5186

South Asian (SAS) AF: 0.201 AC: 969 AN: 4824

European-Finnish (FIN) AF: 0.0484 AC: 513 AN: 10600

Middle Eastern (MID) AF: 0.0782 AC: 23 AN: 294

European-Non Finnish (NFE) AF: 0.0678 AC: 4610 AN: 68030

Other (OTH) AF: 0.0898 AC: 190 AN: 2116

Alfa AF: 0.0656 Hom.: 67

Bravo AF: 0.0752

Asia WGS AF: 0.126 AC: 438 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.75
CADD	Benign	13
DANN	Benign	0.88
PhyloP100		0.35

Splicing

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

Other links and lift over

dbSNP: rs1923534; hg19: chr10-81710485;