chr10-79938341-G-A

Variant names:

• chr10-79938341-G-A
• rs2819098
• NM_003019.5:c.752-113C>T

Variant summary

Our verdict is Benign. The variant received -20 ACMG points: 0P and 20B. BP4_Strong BP6_Very_Strong BA1

The NM_003019.5(SFTPD):​c.752-113C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.628 in 882,676 control chromosomes in the GnomAD database, including 176,824 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

• Frequency:
  • Genomes: 𝑓 0.68 (35667 hom., cov: 31)
  • Exomes 𝑓: 0.62 (141157 hom.)
• Consequence: SFTPD NM_003019.5 intron
• Clinical Significance: Benign criteria provided, multiple submitters, no conflicts B:2
• Conservation: PhyloP100: -1.85
• Publications: 3 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 -20 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BP6: Variant 10-79938341-G-A is Benign according to our data. Variant chr10-79938341-G-A is described in ClinVar as Benign. ClinVar VariationId is 1239741.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.818 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_003019.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SFTPD	NM_003019.5	MANE Select	c.752-113C>T		intron	N/A	NP_003010.4

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SFTPD	ENST00000372292.8	TSL:1 MANE Select	c.752-113C>T		intron	N/A	ENSP00000361366.3	P35247
	SFTPD	ENST00000946714.1		c.920-113C>T		intron	N/A	ENSP00000616773.1
	SFTPD	ENST00000946710.1		c.893-113C>T		intron	N/A	ENSP00000616769.1

Frequencies

GnomAD3 genomes AF: 0.677 AC: 102766 AN: 151826 Hom.: 35609 Cov.: 31

Gnomad AFR AF: 0.825

Gnomad AMI AF: 0.623

Gnomad AMR AF: 0.647

Gnomad ASJ AF: 0.639

Gnomad EAS AF: 0.779

Gnomad SAS AF: 0.734

Gnomad FIN AF: 0.592

Gnomad MID AF: 0.697

Gnomad NFE AF: 0.598

Gnomad OTH AF: 0.666

GnomAD4 exome AF: 0.618 AC: 451638 AN: 730732 Hom.: 141157 AF XY: 0.621 AC XY: 232819 AN XY: 374790

African (AFR) AF: 0.827 AC: 14702 AN: 17788

American (AMR) AF: 0.611 AC: 15213 AN: 24908

Ashkenazi Jewish (ASJ) AF: 0.635 AC: 10113 AN: 15914

East Asian (EAS) AF: 0.740 AC: 25814 AN: 34864

South Asian (SAS) AF: 0.718 AC: 40035 AN: 55764

European-Finnish (FIN) AF: 0.606 AC: 20690 AN: 34168

Middle Eastern (MID) AF: 0.657 AC: 2091 AN: 3184

European-Non Finnish (NFE) AF: 0.590 AC: 300260 AN: 508578

Other (OTH) AF: 0.639 AC: 22720 AN: 35564

GnomAD4 genome AF: 0.677 AC: 102889 AN: 151944 Hom.: 35667 Cov.: 31 AF XY: 0.679 AC XY: 50412 AN XY: 74260

African (AFR) AF: 0.825 AC: 34204 AN: 41446

American (AMR) AF: 0.648 AC: 9910 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.639 AC: 2217 AN: 3472

East Asian (EAS) AF: 0.779 AC: 4007 AN: 5142

South Asian (SAS) AF: 0.734 AC: 3534 AN: 4812

European-Finnish (FIN) AF: 0.592 AC: 6226 AN: 10524

Middle Eastern (MID) AF: 0.692 AC: 202 AN: 292

European-Non Finnish (NFE) AF: 0.598 AC: 40607 AN: 67948

Other (OTH) AF: 0.671 AC: 1415 AN: 2110

Alfa AF: 0.652 Hom.: 4376

Bravo AF: 0.685

Asia WGS AF: 0.772 AC: 2685 AN: 3478

ClinVar

ClinVar submissions as Germline

Significance: Benign

Revision: criteria provided, multiple submitters, no conflicts

Pathogenic	VUS	Benign	Condition
-	-	2	not provided (2)

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.18
DANN	Benign	0.52
PhyloP100		-1.9
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

Other links and lift over

dbSNP: rs2819098; hg19: chr10-81698097; COSMIC: COSV64852998; COSMIC: COSV64852998;