6-30936937-G-A

Variant names:

• chr6-30936937-G-A
• rs12697941
• ENST00000850875.1:c.53-264G>A

Variant summary

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

The ENST00000850875.1(ENSG00000310558):​c.53-264G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.186 in 151,986 control chromosomes in the GnomAD database, including 3,147 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 0.19 (3147 hom., cov: 31)
• Consequence: ENSG00000310558 ENST00000850875.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.115
• Publications: 8 publications found

Genes affected

ENSG00000310558 (HGNC:):

SFTA2 (HGNC:18386): (surfactant associated 2) Predicted to be located in Golgi apparatus; extracellular region; and transport vesicle. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.386 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000850875.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000310558	ENST00000850875.1		c.53-264G>A		intron	N/A	ENSP00000520959.1
	SFTA2	ENST00000634371.2	TSL:5	n.514-5142C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.186 AC: 28181 AN: 151868 Hom.: 3132 Cov.: 31

Gnomad AFR AF: 0.132

Gnomad AMI AF: 0.291

Gnomad AMR AF: 0.299

Gnomad ASJ AF: 0.203

Gnomad EAS AF: 0.376

Gnomad SAS AF: 0.402

Gnomad FIN AF: 0.221

Gnomad MID AF: 0.158

Gnomad NFE AF: 0.156

Gnomad OTH AF: 0.180

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

GnomAD4 genome AF: 0.186 AC: 28215 AN: 151986 Hom.: 3147 Cov.: 31 AF XY: 0.195 AC XY: 14495 AN XY: 74296

African (AFR) AF: 0.132 AC: 5458 AN: 41488

American (AMR) AF: 0.299 AC: 4572 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.203 AC: 703 AN: 3470

East Asian (EAS) AF: 0.376 AC: 1937 AN: 5148

South Asian (SAS) AF: 0.401 AC: 1925 AN: 4798

European-Finnish (FIN) AF: 0.221 AC: 2337 AN: 10558

Middle Eastern (MID) AF: 0.160 AC: 47 AN: 294

European-Non Finnish (NFE) AF: 0.156 AC: 10574 AN: 67930

Other (OTH) AF: 0.188 AC: 397 AN: 2112

Alfa AF: 0.177 Hom.: 1149

Bravo AF: 0.185

Asia WGS AF: 0.446 AC: 1550 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	3.6
DANN	Benign	0.49
PhyloP100		0.12

Splicing

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

Other links and lift over

dbSNP: rs12697941; hg19: chr6-30904714;