chr10-79950053-C-T

Variant names:

• chr10-79950053-C-T
• rs1923536
• ENST00000421889.1:n.359C>T

Variant summary

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

The ENST00000421889.1(ENSG00000283913):​n.359C>T 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 0.178 in 151,974 control chromosomes in the GnomAD database, including 3,131 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 (3131 hom., cov: 32)
  • Exomes 𝑓: 0.13 (0 hom.)
• Consequence: ENSG00000283913 ENST00000421889.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -5.26
• 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=-1.03).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.278 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SFTPD	XM_011540087.2	c.-3-3391G>A		intron_variant	Intron 1 of 7		XP_011538389.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000283913	ENST00000421889.1	n.359C>T		non_coding_transcript_exon_variant	Exon 4 of 4	3
ENSG00000283913	ENST00000453174.7	n.987C>T		non_coding_transcript_exon_variant	Exon 8 of 8	2
ENSG00000283913	ENST00000818194.1	n.659C>T		non_coding_transcript_exon_variant	Exon 4 of 4

Frequencies

GnomAD3 genomes AF: 0.178 AC: 27034 AN: 151832 Hom.: 3131 Cov.: 32

Gnomad AFR AF: 0.0507

Gnomad AMI AF: 0.205

Gnomad AMR AF: 0.128

Gnomad ASJ AF: 0.188

Gnomad EAS AF: 0.0540

Gnomad SAS AF: 0.290

Gnomad FIN AF: 0.262

Gnomad MID AF: 0.199

Gnomad NFE AF: 0.254

Gnomad OTH AF: 0.172

GnomAD4 exome AF: 0.125 AC: 3 AN: 24 Hom.: 0 Cov.: 0 AF XY: 0.125 AC XY: 2 AN XY: 16

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) AC: 0 AN: 0

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.136 AC: 3 AN: 22

Other (OTH) AF: 0.00 AC: 0 AN: 2

GnomAD4 genome AF: 0.178 AC: 27035 AN: 151950 Hom.: 3131 Cov.: 32 AF XY: 0.178 AC XY: 13240 AN XY: 74248

African (AFR) AF: 0.0506 AC: 2098 AN: 41464

American (AMR) AF: 0.128 AC: 1954 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.188 AC: 654 AN: 3470

East Asian (EAS) AF: 0.0541 AC: 280 AN: 5174

South Asian (SAS) AF: 0.290 AC: 1396 AN: 4810

European-Finnish (FIN) AF: 0.262 AC: 2762 AN: 10532

Middle Eastern (MID) AF: 0.197 AC: 58 AN: 294

European-Non Finnish (NFE) AF: 0.254 AC: 17283 AN: 67924

Other (OTH) AF: 0.172 AC: 363 AN: 2108

Alfa AF: 0.211 Hom.: 500

Bravo AF: 0.158

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.2
DANN	Benign	0.69
PhyloP100		-5.3

Splicing

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

Other links and lift over

dbSNP: rs1923536; hg19: chr10-81709809;