rs12697941

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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC124901299	XM_047419621.1	c.-182G>A		upstream_gene_variant			XP_047275577.1
LOC124901299	XM_047419622.1	c.-182G>A		upstream_gene_variant			XP_047275578.1
LOC124901299	XM_047419623.1	c.-182G>A		upstream_gene_variant			XP_047275579.1
LOC124901299	XM_047419624.1	c.-182G>A		upstream_gene_variant			XP_047275580.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000310558	ENST00000850875.1	c.53-264G>A		intron_variant	Intron 1 of 2			ENSP00000520959.1
SFTA2	ENST00000634371.2	n.514-5142C>T		intron_variant	Intron 4 of 5	5

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 v4.3

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;