rs958865

Variant names:

• chr10-79948273-C-A
• rs958865
• NM_003019.5:c.-4+793G>T

Your query was ambiguous. Multiple possible variants found:

• chr10-79948273-C-A
• chr10-79948273-C-T

Variant summary

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

The NM_003019.5(SFTPD):​c.-4+793G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.181 in 152,182 control chromosomes in the GnomAD database, including 3,226 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 (3226 hom., cov: 33)
• Consequence: SFTPD NM_003019.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.140

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=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.393 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SFTPD	NM_003019.5	c.-4+793G>T		intron_variant	Intron 1 of 7	ENST00000372292.8	NP_003010.4
SFTPD	XM_011540087.2	c.-3-1611G>T		intron_variant	Intron 1 of 7		XP_011538389.1
SFTPD	XM_011540088.3	c.-4+793G>T		intron_variant	Intron 1 of 6		XP_011538390.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SFTPD	ENST00000372292.8	c.-4+793G>T		intron_variant	Intron 1 of 7	1	NM_003019.5	ENSP00000361366.3
SFTPD	ENST00000444384.3	c.37-1611G>T		intron_variant	Intron 1 of 5	3		ENSP00000394325.1
ENSG00000283913	ENST00000421889.1	n.334-1755C>A		intron_variant	Intron 3 of 3	3
ENSG00000283913	ENST00000453174.7	n.962-1755C>A		intron_variant	Intron 7 of 7	2

Frequencies

GnomAD3 genomes AF: 0.181 AC: 27490 AN: 152062 Hom.: 3217 Cov.: 33

Gnomad AFR AF: 0.283

Gnomad AMI AF: 0.0548

Gnomad AMR AF: 0.233

Gnomad ASJ AF: 0.173

Gnomad EAS AF: 0.407

Gnomad SAS AF: 0.306

Gnomad FIN AF: 0.0614

Gnomad MID AF: 0.187

Gnomad NFE AF: 0.102

Gnomad OTH AF: 0.173

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

GnomAD4 genome AF: 0.181 AC: 27545 AN: 152182 Hom.: 3226 Cov.: 33 AF XY: 0.184 AC XY: 13713 AN XY: 74408

Gnomad4 AFR AF: 0.283 AC: 0.283363 AN: 0.283363

Gnomad4 AMR AF: 0.233 AC: 0.233486 AN: 0.233486

Gnomad4 ASJ AF: 0.173 AC: 0.173099 AN: 0.173099

Gnomad4 EAS AF: 0.407 AC: 0.407171 AN: 0.407171

Gnomad4 SAS AF: 0.305 AC: 0.305383 AN: 0.305383

Gnomad4 FIN AF: 0.0614 AC: 0.0614167 AN: 0.0614167

Gnomad4 NFE AF: 0.102 AC: 0.101529 AN: 0.101529

Gnomad4 OTH AF: 0.179 AC: 0.179147 AN: 0.179147

Alfa AF: 0.0767 Hom.: 139

Bravo AF: 0.198

Asia WGS AF: 0.330 AC: 1143 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	5.3
DANN	Benign	0.81
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs958865; hg19: chr10-81708029;